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See detailGenomic expression evaluation: introduction and perspectives
Ramery, Eve ULg; Bureau, Fabrice ULg; Guyot, Hugues ULg et al

Conference (2010, July)

In a way, disease could be considered as the result of gene expression deregulation. Knowing what genes are expressed in a particular cell or tissue and how they are regulated allow to better understand ... [more ▼]

In a way, disease could be considered as the result of gene expression deregulation. Knowing what genes are expressed in a particular cell or tissue and how they are regulated allow to better understand disease mechanisms. Transcriptomic is the study of the expression of the entire genome. This technical challenge has been rendered possible as different species’ genomes began to be sequenced. Several techniques have rendered efficient this process of measuring simultaneously the expression level of a large number of genes. To date, micro-array technology is probably the best known. However, with the development of more affordable techniques, sequencing/ resequencing could compete with microarrays in the future. All together, these techniques open new ways for early diagnosis and prognosis for the practioner ‘in the field’. [less ▲]

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See detailGenomic integration of bovine leukemia provirus and lack of viral RNA expression in the target cells of cattle with different responses to BLV infection.
Kettmann, Richard; Marbaix, Gérard; Cleuter, Yvette et al

in Leukemia Research (1980), 4

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See detailGenomic location of the bovine growth hormone secretagogue receptor (Ghsr) gene and investigation of genetic polymorphism
Colinet, Frédéric ULg; Vanderick, Sylvie ULg; Charloteaux, Benoît ULg et al

in Animal Biotechnology (2009), 20(1), 28-33

The growth hormone secretagogue receptor (GHSR) is involved in the regulation of energetic homeostasis and GH secretion. In this study, the bovine GHSR gene was mapped to BTA1 between BL26 and BMS4004 ... [more ▼]

The growth hormone secretagogue receptor (GHSR) is involved in the regulation of energetic homeostasis and GH secretion. In this study, the bovine GHSR gene was mapped to BTA1 between BL26 and BMS4004. Two different bovine GHSR CDS (GHSR1a and GHSR1b) were sequenced. Six polymorphisms (five SNPs and one 3-bp indel) were also identified, three of them leading to amino acid variations L24V, D194N, and Del R242. These variations are located in the extracellular N-terminal end, the exoloop 2, and the cytoloop 3 of the receptor, respectively. [less ▲]

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See detailGenomic screening and replication in one data set in family-based association testing
Lange, C.; Van Steen, Kristel ULg; McQueen, M. et al

in Conference Abstract Book (2005)

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See detailGenomic screening and replication using the same data set in family-based association testing
Van Steen, Kristel ULg; McQueen, M. B.; Herbert, A. et al

in Nature Genetics (2005), 37(7), 683-691

The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of ... [more ▼]

The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of analyzing such studies stems from the severe multiple-comparison problem resulting from the analysis of thousands of SNPs. Our methodology for genome- wide family- based association studies, using single SNPs or haplotypes, can identify associations that achieve genome- wide significance. In relation to developing guidelines for our screening tools, we determined lower bounds for the estimated power to detect the gene underlying the disease- susceptibility locus, which hold regardless of the linkage disequilibrium structure present in the data. We also assessed the power of our approach in the presence of multiple disease- susceptibility loci. Our screening tools accommodate genomic control and use the concept of haplotype- tagging SNPs. Our methods use the entire sample and do not require separate screening and validation samples to establish genome- wide significance, as population- based designs do. [less ▲]

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See detailGenomic screening in family-based association testing
Murphy, A.; McGueen, M. B.; Su, J. et al

in Genetic Epidemiology. Supplement (2005), 29

Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of ... [more ▼]

Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of disease susceptibility loci, and identify new genetic determinants of disease. However, the problem of multiple comparisons threatens to diminish any potential gains from this newly available data. To circumvent the multiple comparisons issue, we utilize a recently developed screening technique using family-based association testing. This screening methodology allows for the identification of the most promising single-nucleotide polymorphisms for testing without biasing the nominal significance level of our test statistic. We compare the results of our screening technique across univariate and multivariate family-based association tests. From our analyses, we observe that the screening technique, applied to different settings, is fairly consistent in identifying optimal markers for testing. One of the identified markers, TSC0047225, was significantly associated with both the ttth1 (p=0.004) and ttth1-ttth4 (p=0.004) phenotype(s). We find that both univariate- and multivariate-based screening techniques are powerful tools for detecting an association. [less ▲]

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See detailGenomic screening in family-based association testing
Murphy, A.; McGueen, M. B.; Su, J. et al

in BMC Genetics (2005), 6

Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of ... [more ▼]

Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of disease susceptibility loci, and identify new genetic determinants of disease. However, the problem of multiple comparisons threatens to diminish any potential gains from this newly available data. To circumvent the multiple comparisons issue, we utilize a recently developed screening technique using family-based association testing. This screening methodology allows for the identification of the most promising single-nucleotide polymorphisms for testing without biasing the nominal significance level of our test statistic. We compare the results of our screening technique across univariate and multivariate family-based association tests. From our analyses, we observe that the screening technique, applied to different settings, is fairly consistent in identifying optimal markers for testing. One of the identified markers, TSC0047225, was significantly associated with both the ttth1 (p=0.004) and ttth1-ttth4 (p=0.004) phenotype(s). We find that both univariate- and multivariate-based screening techniques are powerful tools for detecting an association. [less ▲]

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See detailGenomic screening in family-based association testing
Van Steen, Kristel ULg; McQueen, M.; Herbert, A. et al

in Genetic Epidemiology (2004), 27

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See detailGenomic screening in family-based association testing and the multiple testing problem
Van Steen, Kristel ULg; McQueen, M. B.; Herbert, A. et al

in Genetic Epidemiology. Supplement (2005), 28

The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of ... [more ▼]

The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of analyzing such studies stems from the severe multiple-comparison problem resulting from the analysis of thousands of SNPs. Our methodology for genome- wide family- based association studies, using single SNPs or haplotypes, can identify associations that achieve genome- wide significance. In relation to developing guidelines for our screening tools, we determined lower bounds for the estimated power to detect the gene underlying the disease- susceptibility locus, which hold regardless of the linkage disequilibrium structure present in the data. We also assessed the power of our approach in the presence of multiple disease- susceptibility loci. Our screening tools accommodate genomic control and use the concept of haplotype- tagging SNPs. Our methods use the entire sample and do not require separate screening and validation samples to establish genome- wide significance, as population- based designs do. [less ▲]

Detailed reference viewed: 11 (2 ULg)
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See detailGenomic selection and scan for major genes for a new lamb survival trait for the New Zealand sheep industry
Auvray, Benoit; Vanderick, Sylvie ULg; Newman, Sheryl-Anne et al

Poster (2012, July)

Lambing percentage is one of the most significant factors affecting profitability on New Zealand sheep farms. Since the early 1990s, lambing percentage has increased at about 1% per year from a relatively ... [more ▼]

Lambing percentage is one of the most significant factors affecting profitability on New Zealand sheep farms. Since the early 1990s, lambing percentage has increased at about 1% per year from a relatively stable level of approximately 100%, and top performing sheep farms are now consistently achieving 150% or more. As lambing percentage increases, the proportion of ewes bearing twins and triplets increases accordingly. Lamb mortality rate in these multiples is higher than in singles, with triplets being particularly susceptible. Consequently, lamb survival has become increasingly important to the New Zealand sheep industry. Sheep Improvement Ltd. (SIL, New Zealand’s national sheep genetic evaluation system owned by Beef + Lamb NZ) records lamb survival to weaning but genetic improvement has been limited due to the low heritability of the trait and the current method of recording. To address those issues, we have developed an improved survival to weaning trait for industry implementation, which is more accurate and more heritable than the current SIL trait. This poster will present results of applying genome-enabled prediction procedures to the new trait to obtain molecular breeding values. It will also describe results from a genome wide association study using the new trait. [less ▲]

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See detailGenomic selection in French dairy cattle
Boichard, D; Guillaume, François ULg; Baur, A et al

in Animal Production Science (2012), 52(12), 115-120

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See detailGENOMIC SELECTION IN FRENCH DAIRY CATTLE
Boichard, D.; Guillaume, F.; Baur, A. et al

in Proceedings of the 9th World Congress on Genetics Applied to Livestock Production (2010)

Detailed reference viewed: 18 (4 ULg)
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See detailGenomic structure and chromosomal mapping of the mouse transcription factor TEF-5 (Tead3) gene
Jacquemin, Patrick; Chen, Zhi; Martial, Joseph ULg et al

in Mammalian Genome : Official Journal of the International Mammalian Genome Society (1999), 10(6), 632-4

Detailed reference viewed: 5 (0 ULg)
See detailGenomic structure of new Peach Mosaic viroid variants in Tunisia
Fekih Hassen, I.; Massart, Sébastien ULg; Kummert, J. et al

Poster (2006)

Detailed reference viewed: 6 (1 ULg)
See detailGenomic structure of new tunisian peach latent mosaic viroid variants
Fekih Hassen, I.; Massart, Sébastien ULg; Roussel, S. et al

Poster (2006)

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See detailGenomic structure of new Tunisian peach latent mosaic viroid variants.
Hassen, I Fekih; Massart, Sébastien ULg; Roussel, S. et al

in Communications in agricultural and applied biological sciences (2006), 71(3 Pt B), 1257-1265

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See detailGenomic structure, organisation, and promoter analysis of the bovine (Bos taurus) Mx1 gene
Gérardin; Baise, Etienne ULg; Pire, Grégory et al

in Gene (2004), 326

Some MX proteins are known to confer a specific resistance against a panel of single-stranded RNA viruses. Many diseases due to such viruses are known to affect cattle worldwide, raising the possibility ... [more ▼]

Some MX proteins are known to confer a specific resistance against a panel of single-stranded RNA viruses. Many diseases due to such viruses are known to affect cattle worldwide, raising the possibility that the identification of an antiviral isoform of a bovine MX protein would allow the implementation of genetic selection programs aimed at improving innate resistance of cattle. With this potential application in mind, the present study was designed to isolate the bovine Mx1 gene including its promoter region and to investigate its genomic organisation and promoter reactivity. The bovine Mx1 gene is made up of 15 exons. All exon-intron boundaries conformed to the consensus sequences. A PCR product that contained a approximately 1-kb, 5'-flanking region upstream from the putative transcription start site was sequenced. Unexpectedly, this DNA region did not contain TATA or CCAAT motifs. A computer scan of the region disclosed a series of putative binding sites for known cytokines and transcription factors. There was a GAAAN(1-2)GAAA(C/G) motif, typical of an interferon-sensitive responsive element, between -118 and -107 from the putative transcription start site. There were also a NF-kappaB, two interleukin-6 binding sites, two Sp1 sites and five GC-rich boxes. The region also contained 12 stretches of the GAAA type, as described in all IFN-inducible genes. Bovine Mx1 expression was assessed by Northern blotting and immunofluorescence in the Madin Darby bovine kidney cells (MDBK) cell line treated with several stimuli. In conclusion, the bovine Mx1 gene and promoter region share the major structural and functional characteristics displayed by their homologs described in the rainbow trout, chicken, mouse and man. [less ▲]

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See detailGenomic structure, promoter analysis and expression of the porcine (Sus scrofa) TLR4 gene.
Thomas, Anne; Broers, Aurore ULg; Vandegaart, Hélène ULg et al

in Molecular Immunology (2006), 43(6), 653-659

Toll-like receptor 4 (TLR4) is essential for initiating the innate response to lipopolysaccharide (LPS) from Gram-negative bacteria by acting as a signal-transducing receptor. As the pig industry faces a ... [more ▼]

Toll-like receptor 4 (TLR4) is essential for initiating the innate response to lipopolysaccharide (LPS) from Gram-negative bacteria by acting as a signal-transducing receptor. As the pig industry faces a unique array of related pathogens, it is anticipated that the genotype of swine TLR4 could be of crucial importance in future strategies aimed at improving genetic resistance to infectious diseases. In order to help in investigating TLR4 as a candidate disease-resistance gene in pigs, we established its genomic structure and produced sufficient flanking intronic sequences to enable simple PCR amplification of the coding portions of the gene. Expression in different porcine tissues was studied and showed splicing variations in mRNA sequences. The cDNA sequence for poTLR4 contains an open reading frame of 2526bp that codes for 841 aa, 98 and 568bp in the 5'- and 3'-UTRs, respectively. Overall, the general organization of porcine, human, murine, and avian TLR4 genes is quite similar: three exons with the third one very long. A high level of conservation of the size and the sequence, especially for the two last exons and particularly in the sequence corresponding to the LRRs and TIR domain, is observed between species. The important antimicrobial properties of these proteins may account for a conservative selection pressure on these TLR4 coding sequences. Several putative binding sites described in the human and murine promoter of TLR4 genes have been identified in the 5'-flanking region of poTLR4. Conversely, this region lacks a TATA box, consensus initiator sequences, or GC-rich regions. The basic sequence data gathered will allow the establishment of an inventory of naturally occurring variation in porcine TLR4, so that alleles can be tested for disease association studies. [less ▲]

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See detailGenomic structure, promoter analysis, and expression of the porcine (Sus scrofa) Mx1 gene
Thomas, Anne; Palm, Mélanie; Broers, Aurore ULg et al

in Immunogenetics (2006), 58

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus ... [more ▼]

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus could improve the innate resistance of pigs to natural influenza infections. Several issues need to be resolved before efficient large scale screening of the allelic polymorphism at the porcine (Sus scrofa) Mx1 locus can be implemented. First, the Mx1 genomic structure has to be established and sufficient flanking intronic sequences have to be gathered to enable simple PCR amplification of the coding portions of the gene. Then, a basic knowledge of the promoter region needs to be obtained as an allelic variation there can significantly alter absolute levels and/or tissue-specificity of MX protein expression. The results gathered here show that the porcine Mx1 gene and promoter share the major structural and functional characteristics displayed by their homologs described in cattle, mouse, chicken, and man. The crucial function of the proximal interferon-sensitive response elements motif for gene expression is also demonstrated. The sequence data compiled here will allow an extensive analysis of the polymorphisms present among the widest spectrum possible of porcine breeds with the aim to identify an Mx1 allele providing antiviral resistance. [less ▲]

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See detailGénomique des maladies inflammatoires intestinales
Louis, Edouard ULg; Libioulle, Cécile ULg; Reenaers, Catherine ULg et al

in Revue Médicale de Liège (2009), 64

Detailed reference viewed: 66 (18 ULg)