References of "Hugot, Jean-Pierre"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailMolecular reclassification of Crohn's disease: a cautionary note on population stratification.
Maus, Barbel; Jung, Camille; Mahachie John, Jestinah ULg et al

in PloS one (2013), 8(10), 77720

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn's disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic ... [more ▼]

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn's disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility to Crohn's disease is widely acknowledged and has been demonstrated by identification of over 100 CD associated genetic loci. However, relating CD subphenotypes to disease susceptible loci has proven to be a difficult task. In this paper we discuss the use of cluster analysis on genetic markers to identify genetic-based subgroups while taking into account possible confounding by population stratification. We show that it is highly relevant to consider the confounding nature of population stratification in order to avoid that detected clusters are strongly related to population groups instead of disease-specific groups. Therefore, we explain the use of principal components to correct for population stratification while clustering affected individuals into genetic-based subgroups. The principal components are obtained using 30 ancestry informative markers (AIM), and the first two PCs are determined to discriminate between continental origins of the affected individuals. Genotypes on 51 CD associated single nucleotide polymorphisms (SNPs) are used to perform latent class analysis, hierarchical and Partitioning Around Medoids (PAM) cluster analysis within a sample of affected individuals with and without the use of principal components to adjust for population stratification. It is seen that without correction for population stratification clusters seem to be influenced by population stratification while with correction clusters are unrelated to continental origin of individuals. [less ▲]

Detailed reference viewed: 12 (1 ULg)
Full Text
Peer Reviewed
See detailMeta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Anderson, Carl A; Boucher, Gabrielle; Lees, Charlie W et al

in Nature Genetics (2011), 43(3), 246-52

Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association ... [more ▼]

Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 x 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis. [less ▲]

Detailed reference viewed: 20 (5 ULg)
Full Text
Peer Reviewed
See detailResequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease.
Momozawa, Yukihide ULg; Mni, Myriam ULg; Nakamura, Kayo ULg et al

in Nature Genetics (2011), 43(1), 43-7

Genome-wide association studies (GWAS) have identified dozens of risk loci for many complex disorders, including Crohn's disease. However, common disease-associated SNPs explain at most approximately 20 ... [more ▼]

Genome-wide association studies (GWAS) have identified dozens of risk loci for many complex disorders, including Crohn's disease. However, common disease-associated SNPs explain at most approximately 20% of the genetic variance for Crohn's disease. Several factors may account for this unexplained heritability, including rare risk variants not adequately tagged thus far in GWAS. That rare susceptibility variants indeed contribute to variation in multifactorial phenotypes has been demonstrated for colorectal cancer, plasma high-density lipoprotein cholesterol levels, blood pressure, type 1 diabetes, hypertriglyceridemia and, in the case of Crohn's disease, for NOD2 (refs. 14,15). Here we describe the use of high-throughput resequencing of DNA pools to search for rare coding variants influencing susceptibility to Crohn's disease in 63 GWAS-identified positional candidate genes. We identify low frequency coding variants conferring protection against inflammatory bowel disease in IL23R, but we conclude that rare coding variants in positional candidates do not make a large contribution to inherited predisposition to Crohn's disease. [less ▲]

Detailed reference viewed: 81 (31 ULg)
Full Text
Peer Reviewed
See detailRevisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries
Pagès, Marie ULg; Chaval, Yannick; Herbreteau, Vincent et al

Conference (2010, April)

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and ... [more ▼]

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe. We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria. [less ▲]

Detailed reference viewed: 11 (1 ULg)
Full Text
Peer Reviewed
See detailRefining the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries
Pagès, Marie ULg; Chaval, Yannick; Herbreteau, Vincent et al

in BMC Evolutionary Biology (2010), 10(184), 184

Background: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of ... [more ▼]

Background: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNAbarcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe. <br />Results: We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria. <br />Conclusions: Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within Berylmys and Rattus genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences. [less ▲]

Detailed reference viewed: 33 (5 ULg)
Full Text
Peer Reviewed
See detailGenome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
Franke, Andre; McGovern, Dermot P B; Barrett, Jeffrey C et al

in Nature Genetics (2010), 42(12), 1118-25

We undertook a meta-analysis of six Crohn's disease genome-wide association studies (GWAS) comprising 6,333 affected individuals (cases) and 15,056 controls and followed up the top association signals in ... [more ▼]

We undertook a meta-analysis of six Crohn's disease genome-wide association studies (GWAS) comprising 6,333 affected individuals (cases) and 15,056 controls and followed up the top association signals in 15,694 cases, 14,026 controls and 414 parent-offspring trios. We identified 30 new susceptibility loci meeting genome-wide significance (P < 5 x 10). A series of in silico analyses highlighted particular genes within these loci and, together with manual curation, implicated functionally interesting candidate genes including SMAD3, ERAP2, IL10, IL2RA, TYK2, FUT2, DNMT3A, DENND1B, BACH2 and TAGAP. Combined with previously confirmed loci, these results identify 71 distinct loci with genome-wide significant evidence for association with Crohn's disease. [less ▲]

Detailed reference viewed: 76 (10 ULg)
Full Text
Peer Reviewed
See detailRefining the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries
Pagès, Marie ULg; Chaval, Yannick; Waengsothorn, Surachit et al

Poster (2009, August)

Among mammals, rodents are recognized as the major hosts and vectors of zoonoses and represent a serious threat for human health. Because of global change, interactions between hosts and pathogens are ... [more ▼]

Among mammals, rodents are recognized as the major hosts and vectors of zoonoses and represent a serious threat for human health. Because of global change, interactions between hosts and pathogens are dramatically modified leading to new unexpected disease risks. To predict some of these, accurate identification of each rodent at specific level is needed. Among Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of biodiversity facing with a growing economical development, affecting habitats, biodiversity and health but also a hot place of emerging and re-emerging diseases. Rat species were demonstrated as main hosts of pathogens but are difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as promising tools for accurate rat species identifications but their achievement is hampered by the need of reliable identifications as a departure. To provide a rigorous systematic framework for epidemiological surveys, we carried out a taxonomic revision of the Rattini tribe. As morphological characters are misleading, we decided to use the DNA sequence information itself as the primary information source to establish group membership and define species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions and applied the method developed by Pons and colleagues (2006) that determines with no a priori the locations of ancestral nodes defining putative species. To name each cluster recognized as a valid species, we obtained sequence from museum holotype specimen, illustrating how huge opportunities ancient DNA analysis may offer to taxonomists. [less ▲]

Detailed reference viewed: 17 (3 ULg)
Full Text
Peer Reviewed
See detailNew karyotypic data for Asian rodents (Rodentia, Muridae) with the first report of B-chromosomes in the genus Mus
Badenhorst, Daleen; Herbreteau, Vincent; Chaval, Yannick et al

in Journal of Zoology (2009), 279(1), 44-56

Karyotypes of 18 rodent species collected in various localities in Thailand were analysed as part of an epidemiological survey of the region using conventional cytogenetic techniques. The aim was to re ... [more ▼]

Karyotypes of 18 rodent species collected in various localities in Thailand were analysed as part of an epidemiological survey of the region using conventional cytogenetic techniques. The aim was to re-assess the reliability of karyotype-based diagnoses of Thai rodents using an updated taxonomic framework. The species examined include Menetes berdmorei (Sciuridae), Mus caroli, Mus cervicolor and Mus cookii, Hapalomys delacouri, Chiropodomys gliroides, as well as several representatives of most of the lineages of the Rattini tribe, that is Rattus exulans, Rattus losea, Rattus tanezumi, Leopoldamys edwardsi, Leopoldamys neilli, Maxomys surifer, Niviventer fulvescens, Berylmys berdmorei, Berylmys bowersi, Bandicota indica and Bandicota savilei (Muridae). The first descriptions of G- and/or C-banding karyotypes are provided for several of these, that is, B. savilei, L. edwardsi, M. surifer, B. berdmorei, B. bowersi, N. fulvescens and H. delacouri. Although largely in agreement with available data, our findings on chromosome morphology differ slightly from those published for L. edwardsi, M. surifer, B. savilei and the two Berylmys species, B. berdmorei and B. bowersi. In addition, we document the novel finding of B-chromosomes in the genera Berylmys, Bandicota and the emblematic Mus. Importantly, few species-specific chromosomal characteristic could be identified within most of the genera investigated in our study and, in contrast to previous claims, the usefulness of karyotypes for diagnosing these Asian murid species appears to be limited. [less ▲]

Detailed reference viewed: 5 (0 ULg)
Full Text
Peer Reviewed
See detailRodents within the Centre for Thai National Reference Collections (CTNRC), Past, Present and Future
Waengsothorn, Surachit; Kenthao, Anan; Latinne, Alice ULg et al

in Kasetsart Journal. Natural Sciences (2009), 43

The Centre for Thai National Reference Collections (CTNRC) was officially established in 1965, but animal collections in Thailand had been continuously conducted long before this time. This paper gives an ... [more ▼]

The Centre for Thai National Reference Collections (CTNRC) was officially established in 1965, but animal collections in Thailand had been continuously conducted long before this time. This paper gives an historical review of the main steps leading to the constitution of the current collections under the administration of TISTR, with a focus on the rodent collection, which represents about one fifth of the whole mammal specimens. An inventory of the species and genera represented is given. Statistics representing the sampling effort in the different Thai provinces are given. The paper concludes with considerations on the current and future needs and the means necessary to develop and support the efforts of the CTNRC. [less ▲]

Detailed reference viewed: 50 (7 ULg)
Full Text
Peer Reviewed
See detailGenome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
Barrett, Jeffrey C.; Hansoul, Sarah ULg; Nicolae, Dan L. et al

in Nature Genetics (2008), 40(8), 955-62

Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease (a total ... [more ▼]

Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease (a total of 3,230 cases and 4,829 controls) and carried out replication in 3,664 independent cases with a mixture of population-based and family-based controls. The results strongly confirm 11 previously reported loci and provide genome-wide significant evidence for 21 additional loci, including the regions containing STAT3, JAK2, ICOSLG, CDKAL1 and ITLN1. The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development. [less ▲]

Detailed reference viewed: 121 (42 ULg)
Full Text
Peer Reviewed
See detailRecent discoveries of new hantaviruses widen their range and question their origins.
Henttonen, Heikki; Buchy, Philippe; Suputtamongkol, Yupin et al

in Annals of the New York Academy of Sciences (2008), 1149

Hantaviruses belong to the Bunyaviridae family. While usually hosted by wild mammals, they are potentially pathogenic for humans, and several serologically distinct groups associated with different ... [more ▼]

Hantaviruses belong to the Bunyaviridae family. While usually hosted by wild mammals, they are potentially pathogenic for humans, and several serologically distinct groups associated with different syndromes have been identified. Yet, investigations have mostly been conducted where human infections by hantaviruses constitute a real and well-identified public health problem, i.e., the holarctic and neotropical areas. Some hantaviruses have also been described from a Suncus murinus in India and a Bandicota indica in Thailand. In addition, recent investigations in Cambodia revealed new Hantavirus types. More recently, two new Hantavirus species were described: Sangassou from a Hylomyscus simus, and Tanganya from a Crocidura theresae, both from Africa (Guinea), thus strongly questioning the current views about geographic range, evolution, and epidemiology of hantaviruses. In such a framework, we have conducted a survey of Hantavirus diversity in Southeast Asia which allows us to isolate the Thailand virus and address questions about the taxonomy of their rodent hosts. Here we present a molecular analysis of representatives of all currently known Hantavirus species, thus allowing the comparison between the newly described ones with a large range sample of rodent hantaviruses. Our results clearly point to the presence of a particular lineage of hantaviruses in Southeast Asia. It also strongly suggests that new viruses, additional mammalian hosts and different related syndromes in humans are likely to be discovered in the near future, particularly in Southeast Asia and in Africa, where Muridae rodents are highly diversified. Furthermore, additional work is also urgently needed to investigate the hantaviruses associated with Crociduridae and Soricidae. [less ▲]

Detailed reference viewed: 15 (0 ULg)