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  • 1
    Keywords: SURVIVAL ; CELL ; polymorphism ; ELEMENTS ; susceptibility loci ; GENOME-WIDE ASSOCIATION ; MODIFIERS ; EXPRESSION SIGNATURE ; CHIP-SEQ ; GENETIC INTERACTION NETWORKS
    Abstract: While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04 - 1.15, p = 1.9 x 10-4 (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03 - 1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteraction values 〉 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers.
    Type of Publication: Journal article published
    PubMed ID: 25830658
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  • 2
    Publication Date: 2018-04-05
    Description: Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 3
    Publication Date: 2018-04-06
    Description: The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
    Keywords: Evolution, Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-09-06
    Description: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Carretero-Paulet, Lorenzo -- Dereeper, Alexis -- Droc, Gaetan -- Guyot, Romain -- Pietrella, Marco -- Zheng, Chunfang -- Alberti, Adriana -- Anthony, Francois -- Aprea, Giuseppe -- Aury, Jean-Marc -- Bento, Pascal -- Bernard, Maria -- Bocs, Stephanie -- Campa, Claudine -- Cenci, Alberto -- Combes, Marie-Christine -- Crouzillat, Dominique -- Da Silva, Corinne -- Daddiego, Loretta -- De Bellis, Fabien -- Dussert, Stephane -- Garsmeur, Olivier -- Gayraud, Thomas -- Guignon, Valentin -- Jahn, Katharina -- Jamilloux, Veronique -- Joet, Thierry -- Labadie, Karine -- Lan, Tianying -- Leclercq, Julie -- Lepelley, Maud -- Leroy, Thierry -- Li, Lei-Ting -- Librado, Pablo -- Lopez, Loredana -- Munoz, Adriana -- Noel, Benjamin -- Pallavicini, Alberto -- Perrotta, Gaetano -- Poncet, Valerie -- Pot, David -- Priyono -- Rigoreau, Michel -- Rouard, Mathieu -- Rozas, Julio -- Tranchant-Dubreuil, Christine -- VanBuren, Robert -- Zhang, Qiong -- Andrade, Alan C -- Argout, Xavier -- Bertrand, Benoit -- de Kochko, Alexandre -- Graziosi, Giorgio -- Henry, Robert J -- Jayarama -- Ming, Ray -- Nagai, Chifumi -- Rounsley, Steve -- Sankoff, David -- Giuliano, Giovanni -- Albert, Victor A -- Wincker, Patrick -- Lashermes, Philippe -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. ; CIRAD, UMR Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales (AGAP), F-34398 Montpellier, France. ; IRD, UMR Diversite Adaptation et Developpement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Nestle Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oe, BP 49716, 37097 Tours Cedex 2, France. ; ENEA Trisaia Research Center, 75026 Rotondella, Italy. ; Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universitat Bielefeld, Universitatsstrasse 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultat, Universitat Bielefeld, 33594 Bielefeld, Germany. ; Institut National de la Recherche Agronomique (INRA), Unite de Recherches en Genomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China. ; Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Departament de Genetica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain. ; Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia. ; Laboratorio de Genetica Molecular, Nucleo de Biotecnologia (NTBio), Embrapa Recursos Geneticos e Biotecnologia, Final Av. W/5 Norte, Parque Estacao Biologia, Brasilia-DF 70770-917, Brazil. ; CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia. ; Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India. ; Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA. ; BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25190796" target="_blank"〉PubMed〈/a〉
    Keywords: Caffeine/biosynthesis/*genetics ; Coffea/classification/*genetics ; *Evolution, Molecular ; *Genome, Plant ; Methyltransferases/genetics/*physiology ; Phylogeny ; Plant Proteins/genetics/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2012-02-10
    Description: A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683990/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mackay, Trudy F C -- Richards, Stephen -- Stone, Eric A -- Barbadilla, Antonio -- Ayroles, Julien F -- Zhu, Dianhui -- Casillas, Sonia -- Han, Yi -- Magwire, Michael M -- Cridland, Julie M -- Richardson, Mark F -- Anholt, Robert R H -- Barron, Maite -- Bess, Crystal -- Blankenburg, Kerstin Petra -- Carbone, Mary Anna -- Castellano, David -- Chaboub, Lesley -- Duncan, Laura -- Harris, Zeke -- Javaid, Mehwish -- Jayaseelan, Joy Christina -- Jhangiani, Shalini N -- Jordan, Katherine W -- Lara, Fremiet -- Lawrence, Faye -- Lee, Sandra L -- Librado, Pablo -- Linheiro, Raquel S -- Lyman, Richard F -- Mackey, Aaron J -- Munidasa, Mala -- Muzny, Donna Marie -- Nazareth, Lynne -- Newsham, Irene -- Perales, Lora -- Pu, Ling-Ling -- Qu, Carson -- Ramia, Miquel -- Reid, Jeffrey G -- Rollmann, Stephanie M -- Rozas, Julio -- Saada, Nehad -- Turlapati, Lavanya -- Worley, Kim C -- Wu, Yuan-Qing -- Yamamoto, Akihiko -- Zhu, Yiming -- Bergman, Casey M -- Thornton, Kevin R -- Mittelman, David -- Gibbs, Richard A -- GM 45146/GM/NIGMS NIH HHS/ -- R01 GM 059469/GM/NIGMS NIH HHS/ -- R01 GM 085183/GM/NIGMS NIH HHS/ -- R01 GM045146/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Feb 8;482(7384):173-8. doi: 10.1038/nature10811.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA. trudy_mackay@ncsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22318601" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Centromere/genetics ; Chromosomes, Insect/genetics ; Drosophila melanogaster/*genetics ; *Genome-Wide Association Study ; *Genomics ; Genotype ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/*genetics ; Selection, Genetic/genetics ; Starvation/genetics ; Telomere/genetics ; X Chromosome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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