Mario Foglio

McGill Genome Centre

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Marta Gut

Centre for Genomic Regulation

Simon Heath

Centro Nacional de Análisis Genómico

Mark Lathrop

McGill University

Gregg Duester

Sanford Burnham Prebys Medical Discovery Institute

Diana Zélénika

Commissariat à l'Énergie Atomique et aux Énergies Alternatives

Doris Lechner

Centre National de Recherche en Génomique Humaine

Paul Brennan

Centre International de Recherche sur le Cancer

Louise Deltour

Institut Jacques Monod

ДЗ

Давид Заридзе

Russian Cancer Research Center NN Blokhin

James McKay

Centre International de Recherche sur le Cancer

Cooperative Institutions

National Cancer Institute

102

Inserm

National Institutes of Health

Centre National de la Recherche Scientifique

Centre International de Recherche sur le Cancer

Division of Cancer Epidemiology and Genetics

Commissariat à l'Énergie Atomique et aux Énergies Alternatives

Cancer Genetics (United States)

Harvard University

Centre National de Recherche en Génomique Humaine

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Genetic and Haplotypic Structure in 14 European and African Cattle Breeds

Genetics (2007)

Mathieu Gautier Thomas Faraut Katayoun Moazami‐Goudarzi Vincent Navratil Mario Foglio

To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detected in silico from available sequence data using two different methods and genotyped on samples from 14 distinct breeds originating from Europe and Africa. Only 696 SNPs could be validated, confirming the importance of trace-quality information for the in silico detection. Most of the validated SNPs were informative in several breeds and were used for a detailed description of their genetic structure and relationships. Results obtained were in agreement with previous studies performed on microsatellite markers and using larger samples. In addition, the majority of the validated SNPs could be mapped precisely, reaching an average density of one marker every 311 kb. This allowed us to analyze the extent of LD in the different breeds. Decrease of LD with physical distance across breeds revealed footprints of ancestral LD at short distances (<10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kilobases. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of <300,000 SNPs, which should be efficient for mapping purposes in most cattle breeds.

10.1534/genetics.107.075804

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Citations (150)

Correction: A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium

PLoS Genetics (2011)

James McKay Thérèse Truong Valérie Gaborieau Amélie Chabrier Shu‐Chun Chuang

Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease.We conducted a GWAS to identify common genetic variation involved in susceptibility to upper aero-digestive tract (UADT) cancers.Genome-wide genotyping was carried out using the Illumina HumanHap300 beadchips in 2,091 UADT cancer cases and 3,513 controls from two large European multi-centre UADT cancer studies, as well as 4,821 generic controls.The 19 top-ranked variants were investigated further in an additional 6,514 UADT cancer cases and 7,892 controls of European descent from an additional 13 UADT cancer studies participating in the INHANCE consortium.Five common variants presented evidence for significant association in the combined analysis (p#5610 27 ).Two novel variants were identified, a 4q21 variant (rs1494961, p = 1610 28 ) located near DNA repair related genes HEL308 and FAM175A (or Abraxas) and a 12q24 variant (rs4767364, p = 2610 28 ) located in an extended linkage disequilibrium region that contains multiple genes including the aldehyde dehydrogenase 2 (ALDH2) gene.Three remaining variants are located in the ADH gene cluster and were identified previously in a candidate gene study involving some of these samples.The association between these three variants and UADT cancers was independently replicated in 5,092 UADT cancer cases and 6,794 controls nonoverlapping samples presented here (rs1573496-ADH7, p = 5610 28 ; rs1229984-ADH1B, p = 7610 29 ; and rs698-ADH1C, p = 0.02).These results implicate two variants at 4q21 and 12q24 and further highlight three ADH variants in UADT cancer susceptibility.

Genome-wide Association Study

Association (psychology)

10.1371/annotation/9952526f-2f1f-47f3-af0f-1a7cf6f0abc1

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Citations (14)

A role for non-coding Tsix transcription in partitioning chromatin domains within the mouse X-inactivation centre

Epigenetics & Chromatin (2009)

Pablo Navarro Sophie Chantalat Mario Foglio Corinne Chureau Sébastien Vigneau

Abstract Background Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region ( Xic ), the Xist locus, which triggers X-inactivation, is juxtaposed to a large domain of H3K27 trimethylation (H3K27me3). Results We describe here that developmentally regulated transcription of Tsix , a crucial non-coding antisense to Xist , is required to block the spreading of the H3K27me3 domain to the adjacent H3K4me2-rich Xist region. Analyses of a series of distinct Tsix mutations suggest that the underlying mechanism involves the RNA Polymerase II accumulating at the Tsix 3'-end. Furthermore, we report additional unexpected long-range effects of Tsix on the distal sub-region of the Xic , involved in Xic - Xic trans-interactions. Conclusion These data point toward a role for transcription of non-coding RNAs as a developmental strategy for the establishment of functionally distinct domains within the mammalian genome.

XIST

Transcription

RNA polymerase II

10.1186/1756-8935-2-8

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Citations (31)

SNP and haplotype mapping for genetic analysis in the rat

Nature Genetics (2008)

Kathrin Saar Alfred Beck Marie‐Thérèse Bihoreau Ewan Birney Denise Brocklebank

Linkage Disequilibrium

Tag SNP

SNP

SNP genotyping

Inbred strain

Genetic Association

Association mapping

Genetic linkage

10.1038/ng.124

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Citations (191)

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

Nucleic Acids Research (2011)

Lucie Carrière Sébastien Graziani Olivier Alibert Yad Ghavi-Helm Fayçal Boussouar

RNA polymerase (Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of Pol III and its associated transcription factors on the genome of mouse embryonic stem cells using a highly specific tandem ChIP-Seq method. Only a subset of the annotated class III genes was bound and thus transcribed. A few hundred SINEs were associated with the Pol III transcription machinery. We observed that Pol III and its transcription factors were present at 30 unannotated sites on the mouse genome, only one of which was conserved in human. An RNA was associated with >80% of these regions. More than 2200 regions bound by TFIIIC transcription factor were devoid of Pol III. These sites were associated with cohesins and often located close to CTCF-binding sites, suggesting that TFIIIC might cooperate with these factors to organize the chromatin. We also investigated the genome-wide distribution of the ubiquitous TFIIS variant, TCEA1. We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a Pol III transcription factor in mammals.

RNA polymerase III

RNA polymerase II

Transcription

CTCF

10.1093/nar/gkr737

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Citations (74)

Supplementary Material for: A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination

Per Wahlberg L. Strömstedt Xavier Tordoir Mario Foglio S. K. Heath

A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds.

Genetic linkage

Linkage Disequilibrium

Linkage (software)

10.6084/m9.figshare.5104600.v1

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Citations (0)

Completing the chicken genome coverage by radiation hybrid mapping.

HAL (Le Centre pour la Communication Scientifique Directe) (2008)

Mireille Morisson Suzanne Bardes Marine Douaud Frédérique Pitel Sophie Leroux

Radiation hybrid mapping

Source

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Novel Crohn Disease Locus Identified by Genome-Wide Association Maps to a Gene Desert on 5p13.1 and Modulates Expression of PTGER4

PLoS Genetics (2007)

Cécile Libioulle Édouard Louis Sarah Hansoul Cynthia Sandor Frédéric Farnir

To identify novel susceptibility loci for Crohn disease (CD), we undertook a genome-wide association study with more than 300,000 SNPs characterized in 547 patients and 928 controls. We found three chromosome regions that provided evidence of disease association with p-values between 10(-6) and 10(-9). Two of these (IL23R on Chromosome 1 and CARD15 on Chromosome 16) correspond to genes previously reported to be associated with CD. In addition, a 250-kb region of Chromosome 5p13.1 was found to contain multiple markers with strongly suggestive evidence of disease association (including four markers with p < 10(-7)). We replicated the results for 5p13.1 by studying 1,266 additional CD patients, 559 additional controls, and 428 trios. Significant evidence of association (p < 4 x 10(-4)) was found in case/control comparisons with the replication data, while associated alleles were over-transmitted to affected offspring (p < 0.05), thus confirming that the 5p13.1 locus contributes to CD susceptibility. The CD-associated 250-kb region was saturated with 111 SNP markers. Haplotype analysis supports a complex locus architecture with multiple variants contributing to disease susceptibility. The novel 5p13.1 CD locus is contained within a 1.25-Mb gene desert. We present evidence that disease-associated alleles correlate with quantitative expression levels of the prostaglandin receptor EP4, PTGER4, the gene that resides closest to the associated region. Our results identify a major new susceptibility locus for CD, and suggest that genetic variants associated with disease risk at this locus could modulate cis-acting regulatory elements of PTGER4.

Genome-wide Association Study

Genetic Association

SNP

10.1371/journal.pgen.0030058

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Citations (564)

Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight

BMC Genomics (2009)

Per Wahlberg Örjan Carlborg Mario Foglio Xavier Tordoir Ann‐Christine Syvänen

Abstract Background We have performed Quantitative Trait Loci (QTL) analysis of an F 2 intercross between two chicken lines divergently selected for juvenile body-weight. In a previous study 13 identified loci with effects on body-weight, only explained a small proportion of the large variation in the F 2 population. Epistatic interaction analysis however, indicated that a network of interacting loci with large effect contributed to the difference in body-weight of the parental lines. This previous analysis was, however, based on a sparse microsatellite linkage map and the limited coverage could have affected the main conclusions. Here we present a revised QTL analysis based on a high-density linkage map that provided a more complete coverage of the chicken genome. Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines. Results We constructed a linkage map comprising 434 genetic markers, covering 31 chromosomes but leaving seven microchromosomes uncovered. The analysis showed that seven regions harbor QTL that influence growth. The pair-wise interaction analysis identified 15 unique QTL pairs and notable is that nine of those involved interactions with a locus on chromosome 7, forming a network of interacting loci. The analysis of ~13,000 SNPs showed that a substantial proportion of the genetic variation present in the founder population has been lost in either of the two selected lines since ~60% of the SNPs polymorphic among lines showed fixation in one of the lines. With the current marker coverage and QTL map resolution we did not observe clear signs of selective sweeps within QTL intervals. Conclusion The results from the QTL analysis using the new improved linkage map are to a large extent in concordance with our previous analysis of this pedigree. The difference in body-weight between the parental chicken lines is caused by many QTL each with a small individual effect. Although the increased chromosomal marker coverage did not lead to the identification of additional QTL, we were able to refine the localization of QTL. The importance of epistatic interaction as a mechanism contributing significantly to the remarkable selection response was further strengthened because additional pairs of interacting loci were detected with the improved map.

Epistasis

Genetic linkage

Genetic Analysis

Family-based QTL mapping

10.1186/1471-2164-10-248

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Citations (71)

Impaired retinol utilization inAdh4 alcohol dehydrogenase mutant mice

Developmental Genetics (1999)

Louise Deltour Mario Foglio Gregg Duester

Adh4, a member of the mouse alcohol dehydrogenase (ADH) gene family, encodes an enzyme that functions in vitro as a retinol dehydrogenase in the conversion of retinol to retinoic acid, an important developmental signaling molecule. To explore the role of Adh4 in retinoid signaling in vivo, gene targeting was used to create a null mutation at the Adh4 locus. Homozygous Adh4 mutant mice were viable and fertile and demonstrated no obvious defects when maintained on a standard mouse diet. However, when subjected to vitamin A deficiency during gestation, Adh4 mutant mice demonstrated a higher number of stillbirths than did wild-type mice. The proportion of liveborn second generation vitamin A-deficient newborn mice was only 15% for Adh4 mutant mice but 49% for wild-type mice. After retinol administration to vitamin A-deficient dams in order to rescue embryonic development, Adh4 mutant mice demonstrated a higher resorption rate at stage E12.5 (69%), compared with wild-type mice (30%). The relative ability of Adh4 mutant and wild-type mice to metabolize retinol to retinoic acid was measured after administration of a 100-mg/kg dose of retinol. Whereas kidney retinoic acid levels were below the level of detection in all vehicle-treated mice (<1 pmol/g), retinol treatment resulted in very high kidney retinoic acid levels in wild-type mice (273 pmol/g) but 8-fold lower levels in Adh4 mutant mice (32 pmol/g), indicating a defect in metabolism of retinol to retinoic acid. These findings demonstrate that another retinol dehydrogenase can compensate for a lack of Adh4 when vitamin A is sufficient, but that Adh4 helps optimize retinol utilization under conditions of both retinol deficiency and excess. Dev. Genet. 25:1–10, 1999. © 1999 Wiley-Liss, Inc.

Wild type

10.1002/(sici)1520-6408(1999)25:1<1::aid-dvg1>3.0.co;2-w

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Citations (78)