26
|
Ghouzali I, Bahlouli W, Lemaitre C, Azhar S, Meleine M, Ducrotté P, Déchelotte P, Coëffier M. Une supplémentation en glutamine limite l’hyperperméabilité intestinale dans deux modèles murins mimant les symptômes du syndrome de l’intestin irritable. NUTR CLIN METAB 2017. [DOI: 10.1016/j.nupar.2016.10.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Marinosci A, Doit C, Koehl B, Belhacel K, Mariani Kurkdjian P, Melki I, Renaud A, Lemaitre C, Ammar Khodja N, Blachier A, Bonacorsi S, Faye A, Lorrot M. [Nosocomial rotavirus gastroenteritis]. Arch Pediatr 2016; 23:1118-1123. [PMID: 27642146 DOI: 10.1016/j.arcped.2016.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 06/22/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022]
Abstract
Rotavirus is the most common cause of gastroenteritis in children requiring hospitalization. It is a very resistant and contagious virus causing nosocomial gastroenteritis. In France, the vaccine against rotavirus has been available since 2006, but the vaccine is not recommended for infant vaccination. The aim of this retrospective study was to describe nosocomial rotavirus gastroenteritis (NRGE) and to assess its impact on children hospitalized in the General Pediatrics Department of Robert-Debré Hospital (Paris) between 1 January 2009 and 31 December 2013. We analyzed the demographic characteristics of children (age, term birth, underlying diseases) and the severity of the NRGE (oral or intravenous hydration), and assessed whether these children could benefit from vaccination against rotavirus. RESULTS One hundred thirty-six children presented nosocomial rotavirus infection, with an incidence of 2.5 NRGE per 1000 days of hospitalization. The incidence of NRGE was stable between 2009 and 2013 despite the introduction of specific hygiene measures. The average age of the children was 7 months (range: 0.5-111 months). Most often NRGE occurred in children hospitalized for respiratory diseases (65% of cases) and requiring prolonged hospitalization (median: 18 days). One-third of children were born premature (25%). Hydration was oral in 80 patients (59%), by intravenous infusion in 18 patients (13%), and intraosseous in one patient. Half of the patients were aged less than 5 months and could benefit from the protection afforded by vaccination. CONCLUSION NRGE are common. Rotavirus mass vaccination should have a positive impact on the incidence of NRGE by reducing the number of children hospitalized for gastroenteritis, therefore indirectly reducing the number of hospital cross-infections of hospitalized children who are too young to be vaccinated.
Collapse
|
28
|
Durand L, Sachs P, Lemaitre C, Lorrot M, Bassehila J, Bourdon O, Prot-Labarthe S. NSAIDs in paediatrics: caution with varicella! Int J Clin Pharm 2016; 37:975-7. [PMID: 26297238 DOI: 10.1007/s11096-015-0184-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Anti-inflammatory drugs have been suspected on several occasions to have promoted development of bacterial infection among varicella patients. Some countries have not implemented childhood varicella vaccination. Three cases in our hospital suggested the predisposing role of NSAIDs in varicella patient deterioration. Open access to these drugs widely increases their use and patient information should be continually provided in the medical offices and at dispensing pharmacy counters. Taking account of the benefit/risk balance and applying the simple precautionary principle, it would be appropriate to be cautious about the use of NSAIDs in the paediatric population.
Collapse
|
29
|
Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P. Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. Gigascience 2016; 5:9. [PMID: 26870323 PMCID: PMC4750246 DOI: 10.1186/s13742-015-0105-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/07/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. FINDINGS Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. CONCLUSIONS With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.
Collapse
|
30
|
Benoit G, Lemaitre C, Lavenier D, Drezen E, Dayris T, Uricaru R, Rizk G. Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics 2015; 16:288. [PMID: 26370285 PMCID: PMC4570262 DOI: 10.1186/s12859-015-0709-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/17/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip method. RESULTS We present a novel reference-free method meant to compress data issued from high throughput sequencing technologies. Our approach, implemented in the software LEON, employs techniques derived from existing assembly principles. The method is based on a reference probabilistic de Bruijn Graph, built de novo from the set of reads and stored in a Bloom filter. Each read is encoded as a path in this graph, by memorizing an anchoring kmer and a list of bifurcations. The same probabilistic de Bruijn Graph is used to perform a lossy transformation of the quality scores, which allows to obtain higher compression rates without losing pertinent information for downstream analyses. CONCLUSIONS LEON was run on various real sequencing datasets (whole genome, exome, RNA-seq or metagenomics). In all cases, LEON showed higher overall compression ratios than state-of-the-art compression software. On a C. elegans whole genome sequencing dataset, LEON divided the original file size by more than 20. LEON is an open source software, distributed under GNU affero GPL License, available for download at http://gatb.inria.fr/software/leon/.
Collapse
|
31
|
Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ, d'Alençon E. Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species? Genetica 2015; 143:305-16. [PMID: 25694156 PMCID: PMC4419160 DOI: 10.1007/s10709-015-9829-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022]
Abstract
The moth Spodoptera frugiperda is a well-known pest of crops throughout the Americas, which consists of two strains adapted to different host-plants: the first feeds preferentially on corn, cotton and sorghum whereas the second is more associated with rice and several pasture grasses. Though morphologically indistinguishable, they exhibit differences in their mating behavior, pheromone compositions, and show development variability according to the host-plant. Though the latter suggest that both strains are different species, this issue is still highly controversial because hybrids naturally occur in the wild, not to mention the discrepancies among published results concerning mating success between the two strains. In order to clarify the status of the two host-plant strains of S. frugiperda, we analyze features that possibly reflect the level of post-zygotic isolation: (1) first generation (F1) hybrid lethality and sterility; (2) patterns of meiotic segregation of hybrids in reciprocal second generation (F2), as compared to the meiosis of the two parental strains. We found a significant reduction of mating success in F1 in one direction of the cross and a high level of microsatellite markers showing transmission ratio distortion in the F2 progeny. Our results support the existence of post-zygotic reproductive isolation between the two laboratory strains and are in accordance with the marked level of genetic differentiation that was recovered between individuals of the two strains collected from the field. Altogether these results provide additional evidence in favor of a sibling species status for the two strains.
Collapse
|
32
|
Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P. Reference-free detection of isolated SNPs. Nucleic Acids Res 2014; 43:e11. [PMID: 25404127 PMCID: PMC4333369 DOI: 10.1093/nar/gku1187] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, discoSnp, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, discoSnp ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, discoSnp requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism.
Collapse
|
33
|
Gouin A, Legeai F, Nouhaud P, Whibley A, Simon JC, Lemaitre C. Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads. Heredity (Edinb) 2014; 114:494-501. [PMID: 25269379 DOI: 10.1038/hdy.2014.85] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/29/2014] [Accepted: 08/04/2014] [Indexed: 12/30/2022] Open
Abstract
Unmapped reads are often discarded from the analysis of whole-genome re-sequencing, but new biological information and insights can be uncovered through their analysis. In this paper, we investigate unmapped reads from the re-sequencing data of 33 pea aphid genomes from individuals specialized on different host plants. The unmapped reads for each individual were retrieved following mapping to the Acyrthosiphon pisum reference genome and its mitochondrial and symbiont genomes. These sets of unmapped reads were then cross-compared, revealing that a significant number of these unmapped sequences were conserved across individuals. Interestingly, sequences were most commonly shared between individuals adapted to the same host plant, suggesting that these sequences may contribute to the divergence between host plant specialized biotypes. Analysis of the contigs obtained from assembling the unmapped reads pooled by biotype allowed us to recover some divergent genomic regions previously excluded from analysis and to discover putative novel sequences of A. pisum and its symbionts. In conclusion, this study emphasizes the interest of the unmapped component of re-sequencing data sets and the potential loss of important information. We here propose strategies to aid the capture and interpretation of this information.
Collapse
|
34
|
Rizk G, Gouin A, Chikhi R, Lemaitre C. MindTheGap: integrated detection and assembly of short and long insertions. Bioinformatics 2014; 30:3451-7. [PMID: 25123898 PMCID: PMC4253827 DOI: 10.1093/bioinformatics/btu545] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Motivation: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. Results: We propose here an original method, called MindTheGap, for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. MindTheGap uses an efficient k-mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. MindTheGap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, MindTheGap detected and correctly assembled insertions >1 kb, using at most 14 GB of memory. Availability and implementation:http://mindthegap.genouest.org Contact:guillaume.rizk@inria.fr or claire.lemaitre@inria.fr
Collapse
|
35
|
Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D. GATB: Genome Assembly & Analysis Tool Box. ACTA ACUST UNITED AC 2014; 30:2959-61. [PMID: 24990603 PMCID: PMC4184257 DOI: 10.1093/bioinformatics/btu406] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Motivation: Efficient and fast next-generation sequencing (NGS) algorithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. Results: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms with low memory footprints. Availability and implementation: The GATB library is written in C++ and is available at the following Web site http://gatb.inria.fr under the A-GPL license. Contact:lavenier@irisa.fr Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
|
36
|
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P. Compareads: comparing huge metagenomic experiments. BMC Bioinformatics 2012; 13 Suppl 19:S10. [PMID: 23282463 PMCID: PMC3526429 DOI: 10.1186/1471-2105-13-s19-s10] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background Nowadays, metagenomic sample analyses are mainly achieved by comparing them with a priori knowledge stored in data banks. While powerful, such approaches do not allow to exploit unknown and/or "unculturable" species, for instance estimated at 99% for Bacteria. Methods This work introduces Compareads, a de novo comparative metagenomic approach that returns the reads that are similar between two possibly metagenomic datasets generated by High Throughput Sequencers. One originality of this work consists in its ability to deal with huge datasets. The second main contribution presented in this paper is the design of a probabilistic data structure based on Bloom filters enabling to index millions of reads with a limited memory footprint and a controlled error rate. Results We show that Compareads enables to retrieve biological information while being able to scale to huge datasets. Its time and memory features make Compareads usable on read sets each composed of more than 100 million Illumina reads in a few hours and consuming 4 GB of memory, and thus usable on today's personal computers. Conclusion Using a new data structure, Compareads is a practical solution for comparing de novo huge metagenomic samples. Compareads is released under the CeCILL license and can be freely downloaded from http://alcovna.genouest.org/compareads/.
Collapse
|
37
|
Lemaitre C, Barré A, Citti C, Tardy F, Thiaucourt F, Sirand-Pugnet P, Thébault P. A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships. BMC Bioinformatics 2011; 12:457. [PMID: 22115330 PMCID: PMC3248887 DOI: 10.1186/1471-2105-12-457] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/24/2011] [Indexed: 11/10/2022] Open
Abstract
Background Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to accurately estimate alignment scores and statistical significance with sequences sharing marked compositional biases. Results We present a general and simple methodology to build matrices that are especially fitted to the compositional bias of proteins. Our approach is inspired from the one used to build the BLOSUM matrices and is based on learning substitution and amino acid frequencies on real sequences with the corresponding compositional bias. We applied it to the large scale comparison of Mollicute AT-rich genomes. The new matrix, MOLLI60, was used to predict pairwise orthology relationships, as well as homolog families among 24 Mollicute genomes. We show that this new matrix enables to better discriminate between true and false orthologs and improves the clustering of homologous proteins, with respect to the use of the classical matrix BLOSUM62. Conclusions We show in this paper that well-fitted matrices can improve the predictions of orthologous and homologous relationships among proteins with a similar compositional bias. With the ever-increasing number of sequenced genomes, our approach could prove valuable in numerous comparative studies focusing on atypical genomes.
Collapse
|
38
|
Véron AS, Lemaitre C, Gautier C, Lacroix V, Sagot MF. Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny. BMC Genomics 2011; 12:303. [PMID: 21663614 PMCID: PMC3132170 DOI: 10.1186/1471-2164-12-303] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 06/10/2011] [Indexed: 12/01/2022] Open
Abstract
Background Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements also play a major role in the reorganisation of loci proximities. Whether the same loci are involved in both mechanisms has been studied in the case of somatic rearrangements, but never from an evolutionary standpoint. Results In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting from evolutionary rearrangements which occurred since the split of the human and mouse lineages. Surprisingly, we found that two loci distant in the human genome but adjacent in the mouse genome are significantly more often observed in close proximity in the human nucleus than expected. Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions. Conclusions These findings strongly suggest that part of the 3D organisation of chromosomes may be conserved across very large evolutionary distances. To characterise this phenomenon, we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case.
Collapse
|
39
|
Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF. Cassis: detection of genomic rearrangement breakpoints. Bioinformatics 2010; 26:1897-8. [PMID: 20576622 PMCID: PMC2905553 DOI: 10.1093/bioinformatics/btq301] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Summary: Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints. Availability: Perl and R scripts are freely available for download at http://pbil.univ-lyon1.fr/software/Cassis/. Documentation with methodological background, technical aspects, download and setup instructions, as well as examples of applications are available together with the package. The package was tested on Linux and Mac OS environments and is distributed under the GNU GPL License. Contact:Marie-France.Sagot@inria.fr Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
|
40
|
Lemaitre C, Doit C, Ilharreborde B, Ferroni A, Vu-Thien H, Glorion C, Raymond J, Faye A, Mary P, Seringe R, Pennecot G, Bingen E, Lorrot M. CL120 - Infections ostéo-articulaires de l’enfant à Streptococcus pneumoniae. Arch Pediatr 2010. [DOI: 10.1016/s0929-693x(10)70336-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
41
|
Lemaitre C, Zaghloul L, Sagot MF, Gautier C, Arneodo A, Tannier E, Audit B. Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genomics 2009; 10:335. [PMID: 19630943 PMCID: PMC2722678 DOI: 10.1186/1471-2164-10-335] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 07/24/2009] [Indexed: 11/21/2022] Open
Abstract
Background The Intergenic Breakage Model, which is the current model of structural genome evolution, considers that evolutionary rearrangement breakages happen with a uniform propensity along the genome but are selected against in genes, their regulatory regions and in-between. However, a growing body of evidence shows that there exists regions along mammalian genomes that present a high susceptibility to breakage. We reconsidered this question taking advantage of a recently published methodology for the precise detection of rearrangement breakpoints based on pairwise genome comparisons. Results We applied this methodology between the genome of human and those of five sequenced eutherian mammals which allowed us to delineate evolutionary breakpoint regions along the human genome with a finer resolution (median size 26.6 kb) than obtained before. We investigated the distribution of these breakpoints with respect to genome organisation into domains of different activity. In agreement with the Intergenic Breakage Model, we observed that breakpoints are under-represented in genes. Surprisingly however, the density of breakpoints in small intergenes (1 per Mb) appears significantly higher than in gene deserts (0.1 per Mb). More generally, we found a heterogeneous distribution of breakpoints that follows the organisation of the genome into isochores (breakpoints are more frequent in GC-rich regions). We then discuss the hypothesis that regions with an enhanced susceptibility to breakage correspond to regions of high transcriptional activity and replication initiation. Conclusion We propose a model to describe the heterogeneous distribution of evolutionary breakpoints along human chromosomes that combines natural selection and a mutational bias linked to local open chromatin state.
Collapse
|
42
|
Lemaitre C, Braga MDV, Gautier C, Sagot MF, Tannier E, Marais GAB. Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes. Genome Biol Evol 2009; 1:56-66. [PMID: 20333177 PMCID: PMC2817401 DOI: 10.1093/gbe/evp006] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2009] [Indexed: 12/23/2022] Open
Abstract
The human sex chromosomes have stopped recombining gradually, which has left five evolutionary strata on the X chromosome. Y inversions are thought to have suppressed X–Y recombination but clear evidence is missing. Here, we looked for such evidence by focusing on a region—the X-added region (XAR)—that includes the pseudoautosomal region and the most recent strata 3 to 5. We estimated and analyzed the whole set of parsimonious scenarios of Y inversions given the gene order in XAR and its Y homolog. Comparing these to scenarios for simulated sequences suggests that the strata 4 and 5 were formed by Y inversions. By comparing the X and Y DNA sequences, we found clear evidence of two Y inversions associated with duplications that coincide with the boundaries of strata 4 and 5. Divergence between duplicates is in agreement with the timing of strata 4 and 5 formation. These duplicates show a complex pattern of gene conversion that resembles the pattern previously found for AMELXY, a stratum 3 locus. This suggests that this locus—despite AMELY being unbroken—was possibly involved in a Y inversion that formed stratum 3. However, no clear evidence supporting the formation of stratum 3 by a Y inversion was found, probably because this stratum is too old for such an inversion to be detectable. Our results strongly support the view that the most recent human strata have arisen by Y inversions and suggest that inversions have played a major role in the differentiation of our sex chromosomes.
Collapse
|
43
|
Lemaitre C, Tannier E, Gautier C, Sagot MF. Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinformatics 2008; 9:286. [PMID: 18564416 PMCID: PMC2443379 DOI: 10.1186/1471-2105-9-286] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 06/18/2008] [Indexed: 11/14/2022] Open
Abstract
Background Genomes undergo large structural changes that alter their organisation. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. We developed a method to precisely delimit rearrangement breakpoints on a genome by comparison with the genome of a related species. Contrary to current methods which search for synteny blocks and simply return what remains in the genome as breakpoints, we propose to go further and to investigate the breakpoints themselves in order to refine them. Results Given some reliable and non overlapping synteny blocks, the core of the method consists in refining the regions that are not contained in them. By aligning each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Since this method requires as input synteny blocks with some properties which, though they appear natural, are not verified by current methods for detecting such blocks, we further give a formal definition and provide an algorithm to compute them. The whole method is applied to delimit breakpoints on the human genome when compared to the mouse and dog genomes. Among the 355 human-mouse and 240 human-dog breakpoints, 168 and 146 respectively span less than 50 Kb. We compared the resulting breakpoints with some publicly available ones and show that we achieve a better resolution. Furthermore, we suggest that breakpoints are rarely reduced to a point, and instead consist in often large regions that can be distinguished from the sequences around in terms of segmental duplications, similarity with related species, and transposable elements. Conclusion Our method leads to smaller breakpoints than already published ones and allows for a better description of their internal structure. In the majority of cases, our refined regions of breakpoint exhibit specific biological properties (no similarity, presence of segmental duplications and of transposable elements). We hope that this new result may provide some insight into the mechanism and evolutionary properties of chromosomal rearrangements.
Collapse
|
44
|
Lemaitre C, Ducos de Lahitte G, Fardeau C, Bodaghi B, Tadayoni R, Gaudric A. 269 Analyse de l’imagerie et de l’épidémiologie au cours du syndrome d’IRVAN : à propos de 4 cas. J Fr Ophtalmol 2007. [DOI: 10.1016/s0181-5512(07)80081-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
45
|
Bodaghi B, Gendron G, Wechsler B, Terrada C, Cassoux N, Huong DLT, Lemaitre C, Fradeau C, LeHoang P, Piette JC. Efficacy of interferon alpha in the treatment of refractory and sight threatening uveitis: a retrospective monocentric study of 45 patients. Br J Ophthalmol 2006; 91:335-9. [PMID: 17050581 PMCID: PMC1857681 DOI: 10.1136/bjo.2006.101550] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AIM Severe uveitis is potentially associated with visual impairment or blindness in young patients. Therapeutic strategies remain controversial. The efficacy of interferon alpha-2a (IFN-alpha2a) in severe uveitis, refractory to steroids and conventional immunosuppressive agents, was evaluated. PATIENTS AND METHODS Patients were included after a major relapse of uveitis following corticosteroids and immunosuppressants. IFN-alpha2a (3 million units three times a week) was administered subcutaneously. Efficacy was assessed by improvement in visual acuity, decrease in vitreous haze, resolution of retinal vasculitis and macular oedema, assessed by fundus examination and fluorescein angiography, and decrease in oral prednisone threshold. RESULTS 45 patients were included. Median age was 32.3 years (range 8-58) and sex ratio (F/M) was 0.66. Uveitis was associated with Behçet's disease in 23 cases (51.1%) and with other entities in 22 cases (48.9%). Median duration of uveitis before interferon therapy was 34.9 months (range 3.4-168.7) and an average of 3.26 relapses following corticosteroids and immunosuppressants was noted. Uveitis was controlled in 82.6% of patients with Behçet's disease and 59% of patients with other types of uveitis (p = 0.07). During a mean follow-up of 29.6 months (range 14-55), median oral prednisone threshold decreased significantly from 23.6 mg/day (range 16-45) to 10 mg/d (range 4-14) (p<0.001). Interferon was discontinued in 10 patients (22.2%) with Behçet's disease and in four patients without Behçet's disease. Relapses occurred in four and one cases, respectively. CONCLUSIONS Interferon therapy appears to be an efficient strategy in severe and relapsing forms of Behçet's disease but also in other uveitic entities. However, it seems to act more to suspend rather than cure the disease. Therefore, IFN-alpha2a may be proposed as a secondline strategy after failure of conventional immunosuppressants.
Collapse
|
46
|
Read RW, Yu F, Accorinti M, Bodaghi B, Chee SP, Fardeau C, Goto H, Holland GN, Kawashima H, Kojima E, Lehoang P, Lemaitre C, Okada AA, Pivetti-Pezzi P, Secchi A, See RF, Tabbara KF, Usui M, Rao NA. Evaluation of the effect on outcomes of the route of administration of corticosteroids in acute Vogt-Koyanagi-Harada disease. Am J Ophthalmol 2006; 142:119-24. [PMID: 16815259 DOI: 10.1016/j.ajo.2006.02.049] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 02/17/2006] [Accepted: 02/21/2006] [Indexed: 11/26/2022]
Abstract
PURPOSE To compare the effect on outcomes of the route of administration of corticosteroids in acute Vogt-Koyanagi-Harada disease. DESIGN Retrospective comparative interventional case series. METHODS SETTINGS Nine international uveitis specialty clinics. STUDY POPULATION Forty-eight patients presenting over a three-year period to a study center with acute Vogt-Koyanagi-Harada disease. INTERVENTION Initial treatment with corticosteroid either orally (Oral only group) or intravenously followed by an oral taper (IV+Oral group). MAIN OUTCOME MEASURES Change in visual acuity with treatment; development of ocular complications, including visually significant cataract, choroidal neovascularization, subretinal fibrosis, fundus pigment migration, nummular hypopigmented lesions, and diffuse fundus depigmentation; use of immunosuppressive therapy. RESULTS The Oral only group comprised 15 patients (31%) and the IV+Oral group 33 patients (69%). Median follow-up was 15 months. There was no difference in duration of follow-up between groups (P = .234). There was no difference in the change in visual acuity between groups, adjusting for initial visual acuity (P = .402). There were no differences in the rates of development of visually significant cataract, fundus pigmentary changes, or in the rate of use of subsequent immunosuppressive therapy between treatment groups. No patients developed choroidal neovascularization or subretinal fibrosis over the study period. CONCLUSIONS Route of administration of corticosteroid had no detectable effect on change in visual acuity nor on the development of visually significant complications over the study period. Prospective trials are necessary to address speed of resolution and definitively answer outcome questions.
Collapse
|
47
|
Suna A, Lemaitre C, El Fallah Seghrouchni A. E-commerce using an agent oriented approach. INTELIGENCIA ARTIFICIAL 2006. [DOI: 10.4114/ia.v9i25.773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
48
|
Touitou V, Escande C, Bodaghi B, Cassoux N, Wechsler B, Lemaitre C, Tran THC, Fardeau C, Piette JC, LeHoang P. [Diagnostic and therapeutic management of Vogt-Koyanagi-Harada syndrome]. J Fr Ophtalmol 2005; 28:9-16. [PMID: 15767894 DOI: 10.1016/s0181-5512(05)81020-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE To determine the most efficient diagnostic tools in Vogt-Koyanagi-Harada syndrome, taking into account the international diagnostic criteria, and to evaluate the therapeutic management of these patients. PATIENTS AND METHODS This study examined patients with a suspicion of VKH syndrome who presented between January 2001 and March 2003, including ocular and extraocular evaluation of the disease at the time of diagnosis. Each patient was classified according to the 1978 international diagnostic criteria and the revised 2001 criteria. In most cases, intravenous steroid pulses were administered. Immunosuppressors were initiated when inflammation was not controlled with steroids. RESULTS Twenty-two patients were included. The mean age was 33.5 years (range, 15-49 years). Posterior segment involvement, which was observed in 21 patients, depended on the stage of the disease. Anterior segment inflammation was associated in eleven cases. Neurologic symptoms, including meningitis, cerebrospinal fluid lymphocytic pleocytosis, tinnitus, or hearing loss were observed in 12 patients. Fourteen patients had dermatologic signs. Five patients who developed VKH syndrome did not meet the 1978 criteria, and three patients did not meet the 2001 revised criteria. In 19 cases, intraocular inflammation was controlled with corticosteroids. In three cases, corticosteroids could not be discontinued. These patients were treated with immunosuppressive molecules: azathioprine, cyclophosphamide, interferon alpha. At the end of the follow-up period, inflammation was controlled in all patients. DISCUSSION Revision of the diagnostic criteria provides a more subtle diagnosis of VKH syndrome. However, it is difficult to consider the variability of clinical symptoms during the duration of disease. Corticosteroids must be used at appropriate dosages, followed by slow tapering over 6 months. This attitude seems to reduce the duration of ocular inflammation and decreases the frequency of recurrence. The use of immunomodulating drugs could be reduced by early and appropriate use of systemic steroids. Interferon alpha seems to be a promising alternative in corticoresistant or corticodependent forms of the disease, but further controlled studies are required.
Collapse
|
49
|
Leduc C, Froussart-Maille F, Dariel R, Lemaitre C, Crepy P, Maille M. 553 Une hypertension intracrânienne bénigne (HICB) et double paralysie du VI : traitement et pronostic. J Fr Ophtalmol 2005. [DOI: 10.1016/s0181-5512(05)73672-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
50
|
Froussart-Maille F, Leduc C, Dariel R, Crepy P, Lemaitre C, Maille M. 011 De l’information visuelle à la prise de décision lors du pilotage d’avion. J Fr Ophtalmol 2005. [DOI: 10.1016/s0181-5512(05)74407-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|