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  • 1
    Publication Date: 2010-04-03
    Description: Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892339/" 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/PMC2892339/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wellcome Trust Case Control Consortium -- Craddock, Nick -- Hurles, Matthew E -- Cardin, Niall -- Pearson, Richard D -- Plagnol, Vincent -- Robson, Samuel -- Vukcevic, Damjan -- Barnes, Chris -- Conrad, Donald F -- Giannoulatou, Eleni -- Holmes, Chris -- Marchini, Jonathan L -- Stirrups, Kathy -- Tobin, Martin D -- Wain, Louise V -- Yau, Chris -- Aerts, Jan -- Ahmad, Tariq -- Andrews, T Daniel -- Arbury, Hazel -- Attwood, Anthony -- Auton, Adam -- Ball, Stephen G -- Balmforth, Anthony J -- Barrett, Jeffrey C -- Barroso, Ines -- Barton, Anne -- Bennett, Amanda J -- Bhaskar, Sanjeev -- Blaszczyk, Katarzyna -- Bowes, John -- Brand, Oliver J -- Braund, Peter S -- Bredin, Francesca -- Breen, Gerome -- Brown, Morris J -- Bruce, Ian N -- Bull, Jaswinder -- Burren, Oliver S -- Burton, John -- Byrnes, Jake -- Caesar, Sian -- Clee, Chris M -- Coffey, Alison J -- Connell, John M C -- Cooper, Jason D -- Dominiczak, Anna F -- Downes, Kate -- Drummond, Hazel E -- Dudakia, Darshna -- Dunham, Andrew -- Ebbs, Bernadette -- Eccles, Diana -- Edkins, Sarah -- Edwards, Cathryn -- Elliot, Anna -- Emery, Paul -- Evans, David M -- Evans, Gareth -- Eyre, Steve -- Farmer, Anne -- Ferrier, I Nicol -- Feuk, Lars -- Fitzgerald, Tomas -- Flynn, Edward -- Forbes, Alistair -- Forty, Liz -- Franklyn, Jayne A -- Freathy, Rachel M -- Gibbs, Polly -- Gilbert, Paul -- Gokumen, Omer -- Gordon-Smith, Katherine -- Gray, Emma -- Green, Elaine -- Groves, Chris J -- Grozeva, Detelina -- Gwilliam, Rhian -- Hall, Anita -- Hammond, Naomi -- Hardy, Matt -- Harrison, Pile -- Hassanali, Neelam -- Hebaishi, Husam -- Hines, Sarah -- Hinks, Anne -- Hitman, Graham A -- Hocking, Lynne -- Howard, Eleanor -- Howard, Philip -- Howson, Joanna M M -- Hughes, Debbie -- Hunt, Sarah -- Isaacs, John D -- Jain, Mahim -- Jewell, Derek P -- Johnson, Toby -- Jolley, Jennifer D -- Jones, Ian R -- Jones, Lisa A -- Kirov, George -- Langford, Cordelia F -- Lango-Allen, Hana -- Lathrop, G Mark -- Lee, James -- Lee, Kate L -- Lees, Charlie -- Lewis, Kevin -- Lindgren, Cecilia M -- Maisuria-Armer, Meeta -- Maller, Julian -- Mansfield, John -- Martin, Paul -- Massey, Dunecan C O -- McArdle, Wendy L -- McGuffin, Peter -- McLay, Kirsten E -- Mentzer, Alex -- Mimmack, Michael L -- Morgan, Ann E -- Morris, Andrew P -- Mowat, Craig -- Myers, Simon -- Newman, William -- Nimmo, Elaine R -- O'Donovan, Michael C -- Onipinla, Abiodun -- Onyiah, Ifejinelo -- Ovington, Nigel R -- Owen, Michael J -- Palin, Kimmo -- Parnell, Kirstie -- Pernet, David -- Perry, John R B -- Phillips, Anne -- Pinto, Dalila -- Prescott, Natalie J -- Prokopenko, Inga -- Quail, Michael A -- Rafelt, Suzanne -- Rayner, Nigel W -- Redon, Richard -- Reid, David M -- Renwick -- Ring, Susan M -- Robertson, Neil -- Russell, Ellie -- St Clair, David -- Sambrook, Jennifer G -- Sanderson, Jeremy D -- Schuilenburg, Helen -- Scott, Carol E -- Scott, Richard -- Seal, Sheila -- Shaw-Hawkins, Sue -- Shields, Beverley M -- Simmonds, Matthew J -- Smyth, Debbie J -- Somaskantharajah, Elilan -- Spanova, Katarina -- Steer, Sophia -- Stephens, Jonathan -- Stevens, Helen E -- Stone, Millicent A -- Su, Zhan -- Symmons, Deborah P M -- Thompson, John R -- Thomson, Wendy -- Travers, Mary E -- Turnbull, Clare -- Valsesia, Armand -- Walker, Mark -- Walker, Neil M -- Wallace, Chris -- Warren-Perry, Margaret -- Watkins, Nicholas A -- Webster, John -- Weedon, Michael N -- Wilson, Anthony G -- Woodburn, Matthew -- Wordsworth, B Paul -- Young, Allan H -- Zeggini, Eleftheria -- Carter, Nigel P -- Frayling, Timothy M -- Lee, Charles -- McVean, Gil -- Munroe, Patricia B -- Palotie, Aarno -- Sawcer, Stephen J -- Scherer, Stephen W -- Strachan, David P -- Tyler-Smith, Chris -- Brown, Matthew A -- Burton, Paul R -- Caulfield, Mark J -- Compston, Alastair -- Farrall, Martin -- Gough, Stephen C L -- Hall, Alistair S -- Hattersley, Andrew T -- Hill, Adrian V S -- Mathew, Christopher G -- Pembrey, Marcus -- Satsangi, Jack -- Stratton, Michael R -- Worthington, Jane -- Deloukas, Panos -- Duncanson, Audrey -- Kwiatkowski, Dominic P -- McCarthy, Mark I -- Ouwehand, Willem -- Parkes, Miles -- Rahman, Nazneen -- Todd, John A -- Samani, Nilesh J -- Donnelly, Peter -- 061858/Wellcome Trust/United Kingdom -- 083948/Wellcome Trust/United Kingdom -- 089989/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 17552/Arthritis Research UK/United Kingdom -- CZB/4/540/Chief Scientist Office/United Kingdom -- ETM/137/Chief Scientist Office/United Kingdom -- ETM/75/Chief Scientist Office/United Kingdom -- G0000934/Medical Research Council/United Kingdom -- G0400874/Medical Research Council/United Kingdom -- G0500115/Medical Research Council/United Kingdom -- G0501942/Medical Research Council/United Kingdom -- G0600329/Medical Research Council/United Kingdom -- G0600705/Medical Research Council/United Kingdom -- G0700491/Medical Research Council/United Kingdom -- G0701003/Medical Research Council/United Kingdom -- G0701420/Medical Research Council/United Kingdom -- G0701810/Medical Research Council/United Kingdom -- G0701810(85517)/Medical Research Council/United Kingdom -- G0800383/Medical Research Council/United Kingdom -- G0800509/Medical Research Council/United Kingdom -- G0800759/Medical Research Council/United Kingdom -- G19/9/Medical Research Council/United Kingdom -- G90/106/Medical Research Council/United Kingdom -- G9521010/Medical Research Council/United Kingdom -- MC_UP_A390_1107/Medical Research Council/United Kingdom -- RG/09/012/28096/British Heart Foundation/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Apr 1;464(7289):713-20. doi: 10.1038/nature08979.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360734" target="_blank"〉PubMed〈/a〉
    Keywords: Arthritis, Rheumatoid/genetics ; Case-Control Studies ; Crohn Disease/genetics ; DNA Copy Number Variations/*genetics ; Diabetes Mellitus/genetics ; *Disease ; Gene Frequency/genetics ; Genetic Predisposition to Disease/*genetics ; *Genome-Wide Association Study ; Humans ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Pilot Projects ; Polymorphism, Single Nucleotide/genetics ; Quality Control
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2010-02-05
    Description: Obesity has become a major worldwide challenge to public health, owing to an interaction between the Western 'obesogenic' environment and a strong genetic contribution. Recent extensive genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms associated with obesity, but these loci together account for only a small fraction of the known heritable component. Thus, the 'common disease, common variant' hypothesis is increasingly coming under challenge. Here we report a highly penetrant form of obesity, initially observed in 31 subjects who were heterozygous for deletions of at least 593 kilobases at 16p11.2 and whose ascertainment included cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16,053 individuals from eight European cohorts. These deletions were absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (body mass index (BMI) 〉or= 40 kg m(-2) or BMI standard deviation score 〉or= 4; P = 6.4 x 10(-8), odds ratio 43.0), demonstrating the potential importance in common disease of rare variants with strong effects. This highlights a promising strategy for identifying missing heritability in obesity and other complex traits: cohorts with extreme phenotypes are likely to be enriched for rare variants, thereby improving power for their discovery. Subsequent analysis of the loci so identified may well reveal additional rare variants that further contribute to the missing heritability, as recently reported for SIM1 (ref. 3). The most productive approach may therefore be to combine the 'power of the extreme' in small, well-phenotyped cohorts, with targeted follow-up in case-control and population cohorts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880448/" 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/PMC2880448/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walters, R G -- Jacquemont, S -- Valsesia, A -- de Smith, A J -- Martinet, D -- Andersson, J -- Falchi, M -- Chen, F -- Andrieux, J -- Lobbens, S -- Delobel, B -- Stutzmann, F -- El-Sayed Moustafa, J S -- Chevre, J-C -- Lecoeur, C -- Vatin, V -- Bouquillon, S -- Buxton, J L -- Boute, O -- Holder-Espinasse, M -- Cuisset, J-M -- Lemaitre, M-P -- Ambresin, A-E -- Brioschi, A -- Gaillard, M -- Giusti, V -- Fellmann, F -- Ferrarini, A -- Hadjikhani, N -- Campion, D -- Guilmatre, A -- Goldenberg, A -- Calmels, N -- Mandel, J-L -- Le Caignec, C -- David, A -- Isidor, B -- Cordier, M-P -- Dupuis-Girod, S -- Labalme, A -- Sanlaville, D -- Beri-Dexheimer, M -- Jonveaux, P -- Leheup, B -- Ounap, K -- Bochukova, E G -- Henning, E -- Keogh, J -- Ellis, R J -- Macdermot, K D -- van Haelst, M M -- Vincent-Delorme, C -- Plessis, G -- Touraine, R -- Philippe, A -- Malan, V -- Mathieu-Dramard, M -- Chiesa, J -- Blaumeiser, B -- Kooy, R F -- Caiazzo, R -- Pigeyre, M -- Balkau, B -- Sladek, R -- Bergmann, S -- Mooser, V -- Waterworth, D -- Reymond, A -- Vollenweider, P -- Waeber, G -- Kurg, A -- Palta, P -- Esko, T -- Metspalu, A -- Nelis, M -- Elliott, P -- Hartikainen, A-L -- McCarthy, M I -- Peltonen, L -- Carlsson, L -- Jacobson, P -- Sjostrom, L -- Huang, N -- Hurles, M E -- O'Rahilly, S -- Farooqi, I S -- Mannik, K -- Jarvelin, M-R -- Pattou, F -- Meyre, D -- Walley, A J -- Coin, L J M -- Blakemore, A I F -- Froguel, P -- Beckmann, J S -- 077014/Wellcome Trust/United Kingdom -- 079534/Wellcome Trust/United Kingdom -- 082390/Wellcome Trust/United Kingdom -- 089061/Wellcome Trust/United Kingdom -- 1RL1MH083268-01/MH/NIMH NIH HHS/ -- 5R01HL087679-02/HL/NHLBI NIH HHS/ -- 5R01MH63706:02/MH/NIMH NIH HHS/ -- G0500539/Medical Research Council/United Kingdom -- G0600331/Medical Research Council/United Kingdom -- G0600331(77796)/Medical Research Council/United Kingdom -- G0900554/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Feb 4;463(7281):671-5. doi: 10.1038/nature08727.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Genomic Medicine, Imperial College London, London W12 0NN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130649" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Age of Onset ; Aging ; Body Mass Index ; Case-Control Studies ; Child ; *Chromosome Deletion ; Chromosomes, Human, Pair 16/*genetics ; Cognition Disorders/complications/genetics ; Cohort Studies ; Europe ; Female ; Genome-Wide Association Study ; Heterozygote ; Humans ; Inheritance Patterns/genetics ; Male ; Mutation/genetics ; Obesity/complications/*genetics/*physiopathology ; *Penetrance ; Reproducibility of Results ; Sex Characteristics ; Young Adult
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2017-10-06
    Description: Journal of Proteome Research DOI: 10.1021/acs.jproteome.7b00501
    Print ISSN: 1535-3893
    Electronic ISSN: 1535-3907
    Topics: Chemistry and Pharmacology
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  • 4
    Publication Date: 2009-10-09
    Description: Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330748/" 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/PMC3330748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conrad, Donald F -- Pinto, Dalila -- Redon, Richard -- Feuk, Lars -- Gokcumen, Omer -- Zhang, Yujun -- Aerts, Jan -- Andrews, T Daniel -- Barnes, Chris -- Campbell, Peter -- Fitzgerald, Tomas -- Hu, Min -- Ihm, Chun Hwa -- Kristiansson, Kati -- Macarthur, Daniel G -- Macdonald, Jeffrey R -- Onyiah, Ifejinelo -- Pang, Andy Wing Chun -- Robson, Sam -- Stirrups, Kathy -- Valsesia, Armand -- Walter, Klaudia -- Wei, John -- Wellcome Trust Case Control Consortium -- Tyler-Smith, Chris -- Carter, Nigel P -- Lee, Charles -- Scherer, Stephen W -- Hurles, Matthew E -- 077006/Z/05/Z/Wellcome Trust/United Kingdom -- 077008/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- GM081533/GM/NIGMS NIH HHS/ -- HG004221/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812545" target="_blank"〉PubMed〈/a〉
    Keywords: Continental Population Groups/genetics ; DNA Copy Number Variations/*genetics ; Gene Duplication ; Genetic Predisposition to Disease/*genetics ; Genome, Human/*genetics ; Genome-Wide Association Study ; Genotype ; Haplotypes/genetics ; Humans ; Mutagenesis/*genetics ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2011-09-02
    Description: Both obesity and being underweight have been associated with increased mortality. Underweight, defined as a body mass index (BMI) 〈/= 18.5 kg per m(2) in adults and 〈/= -2 standard deviations from the mean in children, is the main sign of a series of heterogeneous clinical conditions including failure to thrive, feeding and eating disorder and/or anorexia nervosa. In contrast to obesity, few genetic variants underlying these clinical conditions have been reported. We previously showed that hemizygosity of a approximately 600-kilobase (kb) region on the short arm of chromosome 16 causes a highly penetrant form of obesity that is often associated with hyperphagia and intellectual disabilities. Here we show that the corresponding reciprocal duplication is associated with being underweight. We identified 138 duplication carriers (including 132 novel cases and 108 unrelated carriers) from individuals clinically referred for developmental or intellectual disabilities (DD/ID) or psychiatric disorders, or recruited from population-based cohorts. These carriers show significantly reduced postnatal weight and BMI. Half of the boys younger than five years are underweight with a probable diagnosis of failure to thrive, whereas adult duplication carriers have an 8.3-fold increased risk of being clinically underweight. We observe a trend towards increased severity in males, as well as a depletion of male carriers among non-medically ascertained cases. These features are associated with an unusually high frequency of selective and restrictive eating behaviours and a significant reduction in head circumference. Each of the observed phenotypes is the converse of one reported in carriers of deletions at this locus. The phenotypes correlate with changes in transcript levels for genes mapping within the duplication but not in flanking regions. The reciprocal impact of these 16p11.2 copy-number variants indicates that severe obesity and being underweight could have mirror aetiologies, possibly through contrasting effects on energy balance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637175/" 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/PMC3637175/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacquemont, Sebastien -- Reymond, Alexandre -- Zufferey, Flore -- Harewood, Louise -- Walters, Robin G -- Kutalik, Zoltan -- Martinet, Danielle -- Shen, Yiping -- Valsesia, Armand -- Beckmann, Noam D -- Thorleifsson, Gudmar -- Belfiore, Marco -- Bouquillon, Sonia -- Campion, Dominique -- de Leeuw, Nicole -- de Vries, Bert B A -- Esko, Tonu -- Fernandez, Bridget A -- Fernandez-Aranda, Fernando -- Fernandez-Real, Jose Manuel -- Gratacos, Monica -- Guilmatre, Audrey -- Hoyer, Juliane -- Jarvelin, Marjo-Riitta -- Kooy, R Frank -- Kurg, Ants -- Le Caignec, Cedric -- Mannik, Katrin -- Platt, Orah S -- Sanlaville, Damien -- Van Haelst, Mieke M -- Villatoro Gomez, Sergi -- Walha, Faida -- Wu, Bai-Lin -- Yu, Yongguo -- Aboura, Azzedine -- Addor, Marie-Claude -- Alembik, Yves -- Antonarakis, Stylianos E -- Arveiler, Benoit -- Barth, Magalie -- Bednarek, Nathalie -- Bena, Frederique -- Bergmann, Sven -- Beri, Mylene -- Bernardini, Laura -- Blaumeiser, Bettina -- Bonneau, Dominique -- Bottani, Armand -- Boute, Odile -- Brunner, Han G -- Cailley, Dorothee -- Callier, Patrick -- Chiesa, Jean -- Chrast, Jacqueline -- Coin, Lachlan -- Coutton, Charles -- Cuisset, Jean-Marie -- Cuvellier, Jean-Christophe -- David, Albert -- de Freminville, Benedicte -- Delobel, Bruno -- Delrue, Marie-Ange -- Demeer, Benedicte -- Descamps, Dominique -- Didelot, Gerard -- Dieterich, Klaus -- Disciglio, Vittoria -- Doco-Fenzy, Martine -- Drunat, Severine -- Duban-Bedu, Benedicte -- Dubourg, Christele -- El-Sayed Moustafa, Julia S -- Elliott, Paul -- Faas, Brigitte H W -- Faivre, Laurence -- Faudet, Anne -- Fellmann, Florence -- Ferrarini, Alessandra -- Fisher, Richard -- Flori, Elisabeth -- Forer, Lukas -- Gaillard, Dominique -- Gerard, Marion -- Gieger, Christian -- Gimelli, Stefania -- Gimelli, Giorgio -- Grabe, Hans J -- Guichet, Agnes -- Guillin, Olivier -- Hartikainen, Anna-Liisa -- Heron, Delphine -- Hippolyte, Loyse -- Holder, Muriel -- Homuth, Georg -- Isidor, Bertrand -- Jaillard, Sylvie -- Jaros, Zdenek -- Jimenez-Murcia, Susana -- Helas, Geraldine Joly -- Jonveaux, Philippe -- Kaksonen, Satu -- Keren, Boris -- Kloss-Brandstatter, Anita -- Knoers, Nine V A M -- Koolen, David A -- Kroisel, Peter M -- Kronenberg, Florian -- Labalme, Audrey -- Landais, Emilie -- Lapi, Elisabetta -- Layet, Valerie -- Legallic, Solenn -- Leheup, Bruno -- Leube, Barbara -- Lewis, Suzanne -- Lucas, Josette -- MacDermot, Kay D -- Magnusson, Pall -- Marshall, Christian -- Mathieu-Dramard, Michele -- McCarthy, Mark I -- Meitinger, Thomas -- Mencarelli, Maria Antonietta -- Merla, Giuseppe -- Moerman, Alexandre -- Mooser, Vincent -- Morice-Picard, Fanny -- Mucciolo, Mafalda -- Nauck, Matthias -- Ndiaye, Ndeye Coumba -- Nordgren, Ann -- Pasquier, Laurent -- Petit, Florence -- Pfundt, Rolph -- Plessis, Ghislaine -- Rajcan-Separovic, Evica -- Ramelli, Gian Paolo -- Rauch, Anita -- Ravazzolo, Roberto -- Reis, Andre -- Renieri, Alessandra -- Richart, Cristobal -- Ried, Janina S -- Rieubland, Claudine -- Roberts, Wendy -- Roetzer, Katharina M -- Rooryck, Caroline -- Rossi, Massimiliano -- Saemundsen, Evald -- Satre, Veronique -- Schurmann, Claudia -- Sigurdsson, Engilbert -- Stavropoulos, Dimitri J -- Stefansson, Hreinn -- Tengstrom, Carola -- Thorsteinsdottir, Unnur -- Tinahones, Francisco J -- Touraine, Renaud -- Vallee, Louis -- van Binsbergen, Ellen -- Van der Aa, Nathalie -- Vincent-Delorme, Catherine -- Visvikis-Siest, Sophie -- Vollenweider, Peter -- Volzke, Henry -- Vulto-van Silfhout, Anneke T -- Waeber, Gerard -- Wallgren-Pettersson, Carina -- Witwicki, Robert M -- Zwolinksi, Simon -- Andrieux, Joris -- Estivill, Xavier -- Gusella, James F -- Gustafsson, Omar -- Metspalu, Andres -- Scherer, Stephen W -- Stefansson, Kari -- Blakemore, Alexandra I F -- Beckmann, Jacques S -- Froguel, Philippe -- 090532/Wellcome Trust/United Kingdom -- 1RL1MH083268-01/MH/NIMH NIH HHS/ -- 5R01HL087679-02/HL/NHLBI NIH HHS/ -- 5R01MH63706:02/MH/NIMH NIH HHS/ -- AS2173/Autism Speaks/ -- G0500539/Medical Research Council/United Kingdom -- G0600705/Medical Research Council/United Kingdom -- G0801056/Medical Research Council/United Kingdom -- GM061354/GM/NIGMS NIH HHS/ -- MH071425/MH/NIMH NIH HHS/ -- MOP 74502/Canadian Institutes of Health Research/Canada -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 Aug 31;478(7367):97-102. doi: 10.1038/nature10406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21881559" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Aged ; Aging ; Body Height/genetics ; *Body Mass Index ; Case-Control Studies ; Child ; Child, Preschool ; Chromosomes, Human, Pair 16/*genetics ; Cohort Studies ; Comparative Genomic Hybridization ; Developmental Disabilities/genetics ; Energy Metabolism/genetics ; Europe ; Female ; Gene Dosage/*genetics ; Gene Duplication/genetics ; Gene Expression Profiling ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Head/anatomy & histology ; Heterozygote ; Humans ; Infant ; Infant, Newborn ; Male ; Mental Disorders/genetics ; Middle Aged ; Mutation/genetics ; North America ; Obesity/*genetics ; *Phenotype ; RNA, Messenger/analysis/genetics ; Sequence Deletion/genetics ; Thinness/*genetics ; Transcription, Genetic ; Young Adult
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Boraska, V., Jeroncic, A., Colonna, V., Southam, L., Nyholt, D. R., William Rayner, N., Perry, J. R. B., Toniolo, D., Albrecht, E., Ang, W., Bandinelli, S., Barbalic, M., Barroso, I., Beckmann, J. S., Biffar, R., Boomsma, D., Campbell, H., Corre, T., Erdmann, J., Esko, T., Fischer, K., Franceschini, N., Frayling, T. M., Girotto, G., Gonzalez, J. R., Harris, T. B., Heath, A. C., Heid, I. M., Hoffmann, W., Hofman, A., Horikoshi, M., Hua Zhao, J., Jackson, A. U., Hottenga, J.-J., Jula, A., Kahonen, M., Khaw, K.-T., Kiemeney, L. A., Klopp, N., Kutalik, Z., Lagou, V., Launer, L. J., Lehtimaki, T., Lemire, M., Lokki, M.-L., Loley, C., Luan, J., Mangino, M., Mateo Leach, I., Medland, S. E., Mihailov, E., Montgomery, G. W., Navis, G., Newnham, J., Nieminen, M. S., Palotie, A., Panoutsopoulou, K., Peters, A., Pirastu, N., Polasek, O., Rehnstrom, K., Ripatti, S., Ritchie, G. R. S., Rivadeneira, F., Robino, A., Samani, N. J., Shin, S.-Y., Sinisalo, J., Smit, J. H., Soranzo, N., Stolk, L., Swinkels, D. W., Tanaka, T., Teumer, A., Tonjes, A., Traglia, M., Tuomilehto, J., Valsesia, A., van Gilst, W. H., van Meurs, J. B. J., Smith, A. V., Viikari, J., Vink, J. M., Waeber, G., Warrington, N. M., Widen, E., Willemsen, G., Wright, A. F., Zanke, B. W., Zgaga, L., Wellcome Trust Case Control Consortium (WTCCC), Boehnke, M., d'Adamo, A. P., de Geus, E., Demerath, E. W., den Heijer, M., Eriksson, J. G., Ferrucci, L., Gieger, C., Gudnason, V., Hayward, C., Hengstenberg, C., Hudson, T. J., Jarvelin, M.-R., Kogevinas, M., Loos, R. J. F., Martin, N. G., Metspalu, A., Pennell, C. E., Penninx, B. W., Perola, M., Raitakari, O., Salomaa, V., Schreiber, S., Schunkert, H., Spector, T. D., Stumvoll, M., Uitterlinden, A. G., Ulivi, S., van der Harst, P., Vollenweider, P., Volzke, H., Wareham, N. J., Wichmann, H.- E., Wilson, J. F., Rudan, I., Xue, Y., Zeggini, E.
    Oxford University Press
    Publication Date: 2012-10-16
    Description: The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency 〉0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant ( P 〈 5 x 10 –8 ) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across ~115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2015-02-17
    Description: The clinical benefits obtained with rituximab in the treatment of CD20 + B-cell malignancies and of imatinib in the treatment of Phi + leukaemias have opened a new era in oncology, transforming the concepts of tumour-targeted therapies and personalised medicine into reality. Since then, many tumour-targeted monoclonal antibodies and tyrosine kinase inhibitors have been approved for the treatment of cancers. Compared to conventional chemotherapies, these new drugs have more specificity against cancer cells and less systemic toxicities. However, like conventional chemotherapies, they often provide limited therapeutic benefits with short-lasting tumour responses as the vast majority of cancers become resistant to these drugs over time. Therefore, tumour-targeted therapies are an incremental innovation as compared to historical chemotherapies. Recently, a paradigm shift has been brought to the clinic with drugs targeting immune cells rather than cancer cells with the aim of stimulating the anti-tumour immune response of patients against their own cancer. Immunomodulatory drugs such as anti-CTLA4 and anti-PD-1 have generated long-lasting tumour responses when used as single agent in patients with refractory/relapsing cancers such as metastatic melanomas, renal cell carcinoma or non-small-cell lung carcinoma. These new immune-targeted therapies are therefore a disruptive innovation in cancer treatment: they demonstrate that long-lasting clinical benefits could be obtained by targeting molecules involved in the immune tolerance of cancer cells rather than by targeting oncogenic drivers or antigens expressed by cancer cells.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
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  • 8
    Publication Date: 2015-12-23
    Description: Journal of Proteome Research DOI: 10.1021/acs.jproteome.5b00901
    Print ISSN: 1535-3893
    Electronic ISSN: 1535-3907
    Topics: Chemistry and Pharmacology
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  • 9
    Publication Date: 2012-06-16
    Description: Background: Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets. Results: Here we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500 K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550 K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs. Conclusion: Our new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 10
    Publication Date: 2019
    Description: Development of sensitive methods for the determination of E. coli bacteria contamination in water distribution systems is of paramount importance to ensure the microbial safety of drinking water. This work presents a new sensing platform enabling the fast detection of bacteria in field samples by using specific antibodies as the biorecognition element and dark field microscopy as the detection technique. The development of the sensing platform was performed using non-pathogenic bacteria, with the E. coli DH5α strain as the target, and Bacillus sp. 9727 as the negative control. The identification of the captured bacteria was made by analyzing the dark field microscopy images and screening the detected objects by using object circularity and size parameters. Specificity tests revealed the low unspecific attachment of either E. coli over human serum albumin antibodies (negative control for antibody specificity) and of Bacillus sp. over E. coli antibodies. The system performance was tested using field samples, collected from a wastewater treatment plant, and compared with two quantification techniques (i.e., Colilert-18 test and quantitative polymerase chain reaction (qPCR)). The results showed comparable quantification capability. Nevertheless, the present method has the advantage of being faster, is easily adaptable to in-field analysis, and can potentially be extended to the detection of other bacterial strains.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Published by MDPI
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