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  • 1
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    Biological, clinical and population relevance of 95 loci for blood lipids (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-08-06
    Description: Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in 〉100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P 〈 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039276/" 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/PMC3039276/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Teslovich, Tanya M -- Musunuru, Kiran -- Smith, Albert V -- Edmondson, Andrew C -- Stylianou, Ioannis M -- Koseki, Masahiro -- Pirruccello, James P -- Ripatti, Samuli -- Chasman, Daniel I -- Willer, Cristen J -- Johansen, Christopher T -- Fouchier, Sigrid W -- Isaacs, Aaron -- Peloso, Gina M -- Barbalic, Maja -- Ricketts, Sally L -- Bis, Joshua C -- Aulchenko, Yurii S -- Thorleifsson, Gudmar -- Feitosa, Mary F -- Chambers, John -- Orho-Melander, Marju -- Melander, Olle -- Johnson, Toby -- Li, Xiaohui -- Guo, Xiuqing -- Li, Mingyao -- Shin Cho, Yoon -- Jin Go, Min -- Jin Kim, Young -- Lee, Jong-Young -- Park, Taesung -- Kim, Kyunga -- Sim, Xueling -- Twee-Hee Ong, Rick -- Croteau-Chonka, Damien C -- Lange, Leslie A -- Smith, Joshua D -- Song, Kijoung -- Hua Zhao, Jing -- Yuan, Xin -- Luan, Jian'an -- Lamina, Claudia -- Ziegler, Andreas -- Zhang, Weihua -- Zee, Robert Y L -- Wright, Alan F -- Witteman, Jacqueline C M -- Wilson, James F -- Willemsen, Gonneke -- Wichmann, H-Erich -- Whitfield, John B -- Waterworth, Dawn M -- Wareham, Nicholas J -- Waeber, Gerard -- Vollenweider, Peter -- Voight, Benjamin F -- Vitart, Veronique -- Uitterlinden, Andre G -- Uda, Manuela -- Tuomilehto, Jaakko -- Thompson, John R -- Tanaka, Toshiko -- Surakka, Ida -- Stringham, Heather M -- Spector, Tim D -- Soranzo, Nicole -- Smit, Johannes H -- Sinisalo, Juha -- Silander, Kaisa -- Sijbrands, Eric J G -- Scuteri, Angelo -- Scott, James -- Schlessinger, David -- Sanna, Serena -- Salomaa, Veikko -- Saharinen, Juha -- Sabatti, Chiara -- Ruokonen, Aimo -- Rudan, Igor -- Rose, Lynda M -- Roberts, Robert -- Rieder, Mark -- Psaty, Bruce M -- Pramstaller, Peter P -- Pichler, Irene -- Perola, Markus -- Penninx, Brenda W J H -- Pedersen, Nancy L -- Pattaro, Cristian -- Parker, Alex N -- Pare, Guillaume -- Oostra, Ben A -- O'Donnell, Christopher J -- Nieminen, Markku S -- Nickerson, Deborah A -- Montgomery, Grant W -- Meitinger, Thomas -- McPherson, Ruth -- McCarthy, Mark I -- McArdle, Wendy -- Masson, David -- Martin, Nicholas G -- Marroni, Fabio -- Mangino, Massimo -- Magnusson, Patrik K E -- Lucas, Gavin -- Luben, Robert -- Loos, Ruth J F -- Lokki, Marja-Liisa -- Lettre, Guillaume -- Langenberg, Claudia -- Launer, Lenore J -- Lakatta, Edward G -- Laaksonen, Reijo -- Kyvik, Kirsten O -- Kronenberg, Florian -- Konig, Inke R -- Khaw, Kay-Tee -- Kaprio, Jaakko -- Kaplan, Lee M -- Johansson, Asa -- Jarvelin, Marjo-Riitta -- Janssens, A Cecile J W -- Ingelsson, Erik -- Igl, Wilmar -- Kees Hovingh, G -- Hottenga, Jouke-Jan -- Hofman, Albert -- Hicks, Andrew A -- Hengstenberg, Christian -- Heid, Iris M -- Hayward, Caroline -- Havulinna, Aki S -- Hastie, Nicholas D -- Harris, Tamara B -- Haritunians, Talin -- Hall, Alistair S -- Gyllensten, Ulf -- Guiducci, Candace -- Groop, Leif C -- Gonzalez, Elena -- Gieger, Christian -- Freimer, Nelson B -- Ferrucci, Luigi -- Erdmann, Jeanette -- Elliott, Paul -- Ejebe, Kenechi G -- Doring, Angela -- Dominiczak, Anna F -- Demissie, Serkalem -- Deloukas, Panagiotis -- de Geus, Eco J C -- de Faire, Ulf -- Crawford, Gabriel -- Collins, Francis S -- Chen, Yii-der I -- Caulfield, Mark J -- Campbell, Harry -- Burtt, Noel P -- Bonnycastle, Lori L -- Boomsma, Dorret I -- Boekholdt, S Matthijs -- Bergman, Richard N -- Barroso, Ines -- Bandinelli, Stefania -- Ballantyne, Christie M -- Assimes, Themistocles L -- Quertermous, Thomas -- Altshuler, David -- Seielstad, Mark -- Wong, Tien Y -- Tai, E-Shyong -- Feranil, Alan B -- Kuzawa, Christopher W -- Adair, Linda S -- Taylor, Herman A Jr -- Borecki, Ingrid B -- Gabriel, Stacey B -- Wilson, James G -- Holm, Hilma -- Thorsteinsdottir, Unnur -- Gudnason, Vilmundur -- Krauss, Ronald M -- Mohlke, Karen L -- Ordovas, Jose M -- Munroe, Patricia B -- Kooner, Jaspal S -- Tall, Alan R -- Hegele, Robert A -- Kastelein, John J P -- Schadt, Eric E -- Rotter, Jerome I -- Boerwinkle, Eric -- Strachan, David P -- Mooser, Vincent -- Stefansson, Kari -- Reilly, Muredach P -- Samani, Nilesh J -- Schunkert, Heribert -- Cupples, L Adrienne -- Sandhu, Manjinder S -- Ridker, Paul M -- Rader, Daniel J -- van Duijn, Cornelia M -- Peltonen, Leena -- Abecasis, Goncalo R -- Boehnke, Michael -- Kathiresan, Sekar -- 068545/Z/02/Wellcome Trust/United Kingdom -- 076113/B/04/Z/Wellcome Trust/United Kingdom -- 077016/Z/05/Z/Wellcome Trust/United Kingdom -- 079895/Wellcome Trust/United Kingdom -- 1Z01 HG000024/HG/NHGRI NIH HHS/ -- 5R01DK06833603/DK/NIDDK NIH HHS/ -- 5R01DK07568102/DK/NIDDK NIH HHS/ -- 5R01HL087679-02/HL/NHLBI NIH HHS/ -- 5R01HL08770003/HL/NHLBI NIH HHS/ -- 5R01HL08821502/HL/NHLBI NIH HHS/ -- CA 047988/CA/NCI NIH HHS/ -- CZB/4/710/Chief Scientist Office/United Kingdom -- DK062370/DK/NIDDK NIH HHS/ -- DK063491/DK/NIDDK NIH HHS/ -- DK072193/DK/NIDDK NIH HHS/ -- DK078150/DK/NIDDK NIH HHS/ -- DK56350/DK/NIDDK NIH HHS/ -- ES10126/ES/NIEHS NIH HHS/ -- G0000934/Medical Research Council/United Kingdom -- G0401527/Medical Research Council/United Kingdom -- G0601966/Medical Research Council/United Kingdom -- G0700931/Medical Research Council/United Kingdom -- G0701863/Medical Research Council/United Kingdom -- G0801056/Medical Research Council/United Kingdom -- G0801566/Medical Research Council/United Kingdom -- G9521010/Medical Research Council/United Kingdom -- G9521010D/Medical Research Council/United Kingdom -- HHSN268200625226C/PHS HHS/ -- HL 04381/HL/NHLBI NIH HHS/ -- HL 080467/HL/NHLBI NIH HHS/ -- HL-54776/HL/NHLBI NIH HHS/ -- HL085144/HL/NHLBI NIH HHS/ -- K99 HL098364/HL/NHLBI NIH HHS/ -- K99 HL098364-01/HL/NHLBI NIH HHS/ -- K99HL094535/HL/NHLBI NIH HHS/ -- M01-RR00425/RR/NCRR NIH HHS/ -- MC_QA137934/Medical Research Council/United Kingdom -- MC_U106179471/Medical Research Council/United Kingdom -- MC_U106188470/Medical Research Council/United Kingdom -- MC_U127561128/Medical Research Council/United Kingdom -- N01 HC-15103/HC/NHLBI NIH HHS/ -- N01 HC-55222/HC/NHLBI NIH HHS/ -- N01-AG-12100/AG/NIA NIH HHS/ -- N01-HC-25195/HC/NHLBI NIH HHS/ -- N01-HC-35129/HC/NHLBI NIH HHS/ -- N01-HC-45133/HC/NHLBI NIH HHS/ -- N01-HC-55015/HC/NHLBI NIH HHS/ -- N01-HC-55016/HC/NHLBI NIH HHS/ -- N01-HC-55018/HC/NHLBI NIH HHS/ -- N01-HC-55019/HC/NHLBI NIH HHS/ -- N01-HC-55020/HC/NHLBI NIH HHS/ -- N01-HC-55021/HC/NHLBI NIH HHS/ -- N01-HC-55022/HC/NHLBI NIH HHS/ -- N01-HC-75150/HC/NHLBI NIH HHS/ -- N01-HC-85079/HC/NHLBI NIH HHS/ -- N01-HC-85080/HC/NHLBI NIH HHS/ -- N01-HC-85081/HC/NHLBI NIH HHS/ -- N01-HC-85082/HC/NHLBI NIH HHS/ -- N01-HC-85083/HC/NHLBI NIH HHS/ -- N01-HC-85084/HC/NHLBI NIH HHS/ -- N01-HC-85085/HC/NHLBI NIH HHS/ -- N01-HC-85086/HC/NHLBI NIH HHS/ -- N01-HG-65403/HG/NHGRI NIH HHS/ -- N02-HL-6-4278/HL/NHLBI NIH HHS/ -- PG/02/128/British Heart Foundation/United Kingdom -- PG/08/094/British Heart Foundation/United Kingdom -- PG/08/094/26019/British Heart Foundation/United Kingdom -- R01 DK072193/DK/NIDDK NIH HHS/ -- R01 DK078150/DK/NIDDK NIH HHS/ -- R01 HL087647/HL/NHLBI NIH HHS/ -- R01 HL087676/HL/NHLBI NIH HHS/ -- R01 HL089650/HL/NHLBI NIH HHS/ -- R01HL086694/HL/NHLBI NIH HHS/ -- R01HL087641/HL/NHLBI NIH HHS/ -- R01HL087652/HL/NHLBI NIH HHS/ -- R01HL59367/HL/NHLBI NIH HHS/ -- R24 HD050924/HD/NICHD NIH HHS/ -- RC1 HL099634/HL/NHLBI NIH HHS/ -- RC1 HL099634-02/HL/NHLBI NIH HHS/ -- RC1 HL099793/HL/NHLBI NIH HHS/ -- RC2 HL101864,/HL/NHLBI NIH HHS/ -- RC2 HL102419/HL/NHLBI NIH HHS/ -- RG/07/005/23633/British Heart Foundation/United Kingdom -- RR20649/RR/NCRR NIH HHS/ -- SP/08/005/25115/British Heart Foundation/United Kingdom -- T32 GM007092/GM/NIGMS NIH HHS/ -- T32 HG00040/HG/NHGRI NIH HHS/ -- T32HL007208/HL/NHLBI NIH HHS/ -- TW05596/TW/FIC NIH HHS/ -- U01 DK062370/DK/NIDDK NIH HHS/ -- U01 DK062418/DK/NIDDK NIH HHS/ -- U01 HL069757/HL/NHLBI NIH HHS/ -- U01 HL080295/HL/NHLBI NIH HHS/ -- U01HG004402/HG/NHGRI NIH HHS/ -- U54 RR020278/RR/NCRR NIH HHS/ -- UL1RR025005/RR/NCRR NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2010 Aug 5;466(7307):707-13. doi: 10.1038/nature09270.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686565" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/genetics ; Animals ; Asian Continental Ancestry Group/genetics ; Cholesterol, HDL/blood ; Cholesterol, LDL/blood ; Coronary Artery Disease/blood/genetics/therapy ; Europe/ethnology ; European Continental Ancestry Group/genetics ; Female ; Genetic Loci/*genetics ; *Genome-Wide Association Study ; Genotype ; Humans ; Lipid Metabolism/*genetics ; Lipids/*blood ; Liver/metabolism ; Male ; Mice ; N-Acetylgalactosaminyltransferases/genetics/metabolism ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Protein Phosphatase 1/genetics/metabolism ; Reproducibility of Results ; Triglycerides/blood
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Inclusive fitness theory and eusociality (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/" 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/PMC3836173/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbot, Patrick -- Abe, Jun -- Alcock, John -- Alizon, Samuel -- Alpedrinha, Joao A C -- Andersson, Malte -- Andre, Jean-Baptiste -- van Baalen, Minus -- Balloux, Francois -- Balshine, Sigal -- Barton, Nick -- Beukeboom, Leo W -- Biernaskie, Jay M -- Bilde, Trine -- Borgia, Gerald -- Breed, Michael -- Brown, Sam -- Bshary, Redouan -- Buckling, Angus -- Burley, Nancy T -- Burton-Chellew, Max N -- Cant, Michael A -- Chapuisat, Michel -- Charnov, Eric L -- Clutton-Brock, Tim -- Cockburn, Andrew -- Cole, Blaine J -- Colegrave, Nick -- Cosmides, Leda -- Couzin, Iain D -- Coyne, Jerry A -- Creel, Scott -- Crespi, Bernard -- Curry, Robert L -- Dall, Sasha R X -- Day, Troy -- Dickinson, Janis L -- Dugatkin, Lee Alan -- El Mouden, Claire -- Emlen, Stephen T -- Evans, Jay -- Ferriere, Regis -- Field, Jeremy -- Foitzik, Susanne -- Foster, Kevin -- Foster, William A -- Fox, Charles W -- Gadau, Juergen -- Gandon, Sylvain -- Gardner, Andy -- Gardner, Michael G -- Getty, Thomas -- Goodisman, Michael A D -- Grafen, Alan -- Grosberg, Rick -- Grozinger, Christina M -- Gouyon, Pierre-Henri -- Gwynne, Darryl -- Harvey, Paul H -- Hatchwell, Ben J -- Heinze, Jurgen -- Helantera, Heikki -- Helms, Ken R -- Hill, Kim -- Jiricny, Natalie -- Johnstone, Rufus A -- Kacelnik, Alex -- Kiers, E Toby -- Kokko, Hanna -- Komdeur, Jan -- Korb, Judith -- Kronauer, Daniel -- Kummerli, Rolf -- Lehmann, Laurent -- Linksvayer, Timothy A -- Lion, Sebastien -- Lyon, Bruce -- Marshall, James A R -- McElreath, Richard -- Michalakis, Yannis -- Michod, Richard E -- Mock, Douglas -- Monnin, Thibaud -- Montgomerie, Robert -- Moore, Allen J -- Mueller, Ulrich G -- Noe, Ronald -- Okasha, Samir -- Pamilo, Pekka -- Parker, Geoff A -- Pedersen, Jes S -- Pen, Ido -- Pfennig, David -- Queller, David C -- Rankin, Daniel J -- Reece, Sarah E -- Reeve, Hudson K -- Reuter, Max -- Roberts, Gilbert -- Robson, Simon K A -- Roze, Denis -- Rousset, Francois -- Rueppell, Olav -- Sachs, Joel L -- Santorelli, Lorenzo -- Schmid-Hempel, Paul -- Schwarz, Michael P -- Scott-Phillips, Tom -- Shellmann-Sherman, Janet -- Sherman, Paul W -- Shuker, David M -- Smith, Jeff -- Spagna, Joseph C -- Strassmann, Beverly -- Suarez, Andrew V -- Sundstrom, Liselotte -- Taborsky, Michael -- Taylor, Peter -- Thompson, Graham -- Tooby, John -- Tsutsui, Neil D -- Tsuji, Kazuki -- Turillazzi, Stefano -- Ubeda, Francisco -- Vargo, Edward L -- Voelkl, Bernard -- Wenseleers, Tom -- West, Stuart A -- West-Eberhard, Mary Jane -- Westneat, David F -- Wiernasz, Diane C -- Wild, Geoff -- Wrangham, Richard -- Young, Andrew J -- Zeh, David W -- Zeh, Jeanne A -- Zink, Andrew -- BB/H022716/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2011 Mar 24;471(7339):E1-4; author reply E9-10. doi: 10.1038/nature09831.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430721" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; *Genetic Fitness ; Genetics, Population ; Heredity ; Humans ; Male ; *Models, Biological ; Phenotype ; Reproducibility of Results ; *Selection, Genetic ; Sex Ratio
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Genome remodelling in a basal-like breast cancer metastasis and xenograft (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-04-16
    Description: Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872544/" 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/PMC2872544/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ding, Li -- Ellis, Matthew J -- Li, Shunqiang -- Larson, David E -- Chen, Ken -- Wallis, John W -- Harris, Christopher C -- McLellan, Michael D -- Fulton, Robert S -- Fulton, Lucinda L -- Abbott, Rachel M -- Hoog, Jeremy -- Dooling, David J -- Koboldt, Daniel C -- Schmidt, Heather -- Kalicki, Joelle -- Zhang, Qunyuan -- Chen, Lei -- Lin, Ling -- Wendl, Michael C -- McMichael, Joshua F -- Magrini, Vincent J -- Cook, Lisa -- McGrath, Sean D -- Vickery, Tammi L -- Appelbaum, Elizabeth -- Deschryver, Katherine -- Davies, Sherri -- Guintoli, Therese -- Lin, Li -- Crowder, Robert -- Tao, Yu -- Snider, Jacqueline E -- Smith, Scott M -- Dukes, Adam F -- Sanderson, Gabriel E -- Pohl, Craig S -- Delehaunty, Kim D -- Fronick, Catrina C -- Pape, Kimberley A -- Reed, Jerry S -- Robinson, Jody S -- Hodges, Jennifer S -- Schierding, William -- Dees, Nathan D -- Shen, Dong -- Locke, Devin P -- Wiechert, Madeline E -- Eldred, James M -- Peck, Josh B -- Oberkfell, Benjamin J -- Lolofie, Justin T -- Du, Feiyu -- Hawkins, Amy E -- O'Laughlin, Michelle D -- Bernard, Kelly E -- Cunningham, Mark -- Elliott, Glendoria -- Mason, Mark D -- Thompson, Dominic M Jr -- Ivanovich, Jennifer L -- Goodfellow, Paul J -- Perou, Charles M -- Weinstock, George M -- Aft, Rebecca -- Watson, Mark -- Ley, Timothy J -- Wilson, Richard K -- Mardis, Elaine R -- 1 U01 CA114722-01/CA/NCI NIH HHS/ -- 3P50 CA68438/CA/NCI NIH HHS/ -- U01 CA114722/CA/NCI NIH HHS/ -- U10 CA076001/CA/NCI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003079-07/HG/NHGRI NIH HHS/ -- UL1 RR024992/RR/NCRR NIH HHS/ -- UL1 TR000448/TR/NCATS NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):999-1005. doi: 10.1038/nature08989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Center at Washington University, St Louis, Missouri 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393555" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Brain Neoplasms/*genetics/*secondary ; Breast Neoplasms/*genetics/pathology ; DNA Copy Number Variations/genetics ; DNA Mutational Analysis ; Disease Progression ; Female ; Gene Frequency/genetics ; Genome, Human/*genetics ; Genomics ; Humans ; Mutation/*genetics ; *Neoplasm Transplantation ; Translocation, Genetic/genetics ; Transplantation, Heterologous ; alpha Catenin/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus (2011)
    Nature Publishing Group (NPG)
    Details
    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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  • 5
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    Comparative and demographic analysis of orang-utan genomes (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-01-29
    Description: 'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778/" 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/PMC3060778/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Locke, Devin P -- Hillier, LaDeana W -- Warren, Wesley C -- Worley, Kim C -- Nazareth, Lynne V -- Muzny, Donna M -- Yang, Shiaw-Pyng -- Wang, Zhengyuan -- Chinwalla, Asif T -- Minx, Pat -- Mitreva, Makedonka -- Cook, Lisa -- Delehaunty, Kim D -- Fronick, Catrina -- Schmidt, Heather -- Fulton, Lucinda A -- Fulton, Robert S -- Nelson, Joanne O -- Magrini, Vincent -- Pohl, Craig -- Graves, Tina A -- Markovic, Chris -- Cree, Andy -- Dinh, Huyen H -- Hume, Jennifer -- Kovar, Christie L -- Fowler, Gerald R -- Lunter, Gerton -- Meader, Stephen -- Heger, Andreas -- Ponting, Chris P -- Marques-Bonet, Tomas -- Alkan, Can -- Chen, Lin -- Cheng, Ze -- Kidd, Jeffrey M -- Eichler, Evan E -- White, Simon -- Searle, Stephen -- Vilella, Albert J -- Chen, Yuan -- Flicek, Paul -- Ma, Jian -- Raney, Brian -- Suh, Bernard -- Burhans, Richard -- Herrero, Javier -- Haussler, David -- Faria, Rui -- Fernando, Olga -- Darre, Fleur -- Farre, Domenec -- Gazave, Elodie -- Oliva, Meritxell -- Navarro, Arcadi -- Roberto, Roberta -- Capozzi, Oronzo -- Archidiacono, Nicoletta -- Della Valle, Giuliano -- Purgato, Stefania -- Rocchi, Mariano -- Konkel, Miriam K -- Walker, Jerilyn A -- Ullmer, Brygg -- Batzer, Mark A -- Smit, Arian F A -- Hubley, Robert -- Casola, Claudio -- Schrider, Daniel R -- Hahn, Matthew W -- Quesada, Victor -- Puente, Xose S -- Ordonez, Gonzalo R -- Lopez-Otin, Carlos -- Vinar, Tomas -- Brejova, Brona -- Ratan, Aakrosh -- Harris, Robert S -- Miller, Webb -- Kosiol, Carolin -- Lawson, Heather A -- Taliwal, Vikas -- Martins, Andre L -- Siepel, Adam -- Roychoudhury, Arindam -- Ma, Xin -- Degenhardt, Jeremiah -- Bustamante, Carlos D -- Gutenkunst, Ryan N -- Mailund, Thomas -- Dutheil, Julien Y -- Hobolth, Asger -- Schierup, Mikkel H -- Ryder, Oliver A -- Yoshinaga, Yuko -- de Jong, Pieter J -- Weinstock, George M -- Rogers, Jeffrey -- Mardis, Elaine R -- Gibbs, Richard A -- Wilson, Richard K -- G0501331/Medical Research Council/United Kingdom -- HG002238/HG/NHGRI NIH HHS/ -- HG002385/HG/NHGRI NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- P01 AG022064/AG/NIA NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003079-08/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA. dlocke@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21270892" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Centromere/genetics ; Cerebrosides/metabolism ; Chromosomes ; Evolution, Molecular ; Female ; Gene Rearrangement/genetics ; Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Genome/*genetics ; Humans ; Male ; Phylogeny ; Pongo abelii/*genetics ; Pongo pygmaeus/*genetics ; Population Density ; Population Dynamics ; Species Specificity
    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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    The genome of a songbird (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-03
    Description: The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626/" 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/PMC3187626/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Wesley C -- Clayton, David F -- Ellegren, Hans -- Arnold, Arthur P -- Hillier, Ladeana W -- Kunstner, Axel -- Searle, Steve -- White, Simon -- Vilella, Albert J -- Fairley, Susan -- Heger, Andreas -- Kong, Lesheng -- Ponting, Chris P -- Jarvis, Erich D -- Mello, Claudio V -- Minx, Pat -- Lovell, Peter -- Velho, Tarciso A F -- Ferris, Margaret -- Balakrishnan, Christopher N -- Sinha, Saurabh -- Blatti, Charles -- London, Sarah E -- Li, Yun -- Lin, Ya-Chi -- George, Julia -- Sweedler, Jonathan -- Southey, Bruce -- Gunaratne, Preethi -- Watson, Michael -- Nam, Kiwoong -- Backstrom, Niclas -- Smeds, Linnea -- Nabholz, Benoit -- Itoh, Yuichiro -- Whitney, Osceola -- Pfenning, Andreas R -- Howard, Jason -- Volker, Martin -- Skinner, Bejamin M -- Griffin, Darren K -- Ye, Liang -- McLaren, William M -- Flicek, Paul -- Quesada, Victor -- Velasco, Gloria -- Lopez-Otin, Carlos -- Puente, Xose S -- Olender, Tsviya -- Lancet, Doron -- Smit, Arian F A -- Hubley, Robert -- Konkel, Miriam K -- Walker, Jerilyn A -- Batzer, Mark A -- Gu, Wanjun -- Pollock, David D -- Chen, Lin -- Cheng, Ze -- Eichler, Evan E -- Stapley, Jessica -- Slate, Jon -- Ekblom, Robert -- Birkhead, Tim -- Burke, Terry -- Burt, David -- Scharff, Constance -- Adam, Iris -- Richard, Hugues -- Sultan, Marc -- Soldatov, Alexey -- Lehrach, Hans -- Edwards, Scott V -- Yang, Shiaw-Pyng -- Li, Xiaoching -- Graves, Tina -- Fulton, Lucinda -- Nelson, Joanne -- Chinwalla, Asif -- Hou, Shunfeng -- Mardis, Elaine R -- Wilson, Richard K -- BB/D013704/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010652/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F007590/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0175091/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/E/I/00001425/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- P30 DA018310/DA/NIDA NIH HHS/ -- R01 DC007218/DC/NIDCD NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM085233/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 NS045264/NS/NINDS NIH HHS/ -- R01NS051820/NS/NINDS NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@watson.wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360741" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics ; Animals ; Auditory Perception/genetics ; Brain/physiology ; Chickens/genetics ; Evolution, Molecular ; Female ; Finches/*genetics/physiology ; Gene Duplication ; Gene Regulatory Networks/genetics ; Genome/*genetics ; Male ; MicroRNAs/genetics ; Models, Animal ; Multigene Family/genetics ; Retroelements/genetics ; Sex Chromosomes/genetics ; Terminal Repeat Sequences/genetics ; Transcription, Genetic/genetics ; Vocalization, Animal/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    A new highly penetrant form of obesity due to deletions on chromosome 16p11.2 (2010)
    Nature Publishing Group (NPG)
    Details
    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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  • 8
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    A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-11-15
    Description: So far, two genes associated with familial melanoma have been identified, accounting for a minority of genetic risk in families. Mutations in CDKN2A account for approximately 40% of familial cases, and predisposing mutations in CDK4 have been reported in a very small number of melanoma kindreds. Here we report the whole-genome sequencing of probands from several melanoma families, which we performed in order to identify other genes associated with familial melanoma. We identify one individual carrying a novel germline variant (coding DNA sequence c.G1075A; protein sequence p.E318K; rs149617956) in the melanoma-lineage-specific oncogene microphthalmia-associated transcription factor (MITF). Although the variant co-segregated with melanoma in some but not all cases in the family, linkage analysis of 31 families subsequently identified to carry the variant generated a log of odds (lod) score of 2.7 under a dominant model, indicating E318K as a possible intermediate risk variant. Consistent with this, the E318K variant was significantly associated with melanoma in a large Australian case-control sample. Likewise, it was similarly associated in an independent case-control sample from the United Kingdom. In the Australian sample, the variant allele was significantly over-represented in cases with a family history of melanoma, multiple primary melanomas, or both. The variant allele was also associated with increased naevus count and non-blue eye colour. Functional analysis of E318K showed that MITF encoded by the variant allele had impaired sumoylation and differentially regulated several MITF targets. These data indicate that MITF is a melanoma-predisposition gene and highlight the utility of whole-genome sequencing to identify novel rare variants associated with disease susceptibility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266855/" 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/PMC3266855/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yokoyama, Satoru -- Woods, Susan L -- Boyle, Glen M -- Aoude, Lauren G -- MacGregor, Stuart -- Zismann, Victoria -- Gartside, Michael -- Cust, Anne E -- Haq, Rizwan -- Harland, Mark -- Taylor, John C -- Duffy, David L -- Holohan, Kelly -- Dutton-Regester, Ken -- Palmer, Jane M -- Bonazzi, Vanessa -- Stark, Mitchell S -- Symmons, Judith -- Law, Matthew H -- Schmidt, Christopher -- Lanagan, Cathy -- O'Connor, Linda -- Holland, Elizabeth A -- Schmid, Helen -- Maskiell, Judith A -- Jetann, Jodie -- Ferguson, Megan -- Jenkins, Mark A -- Kefford, Richard F -- Giles, Graham G -- Armstrong, Bruce K -- Aitken, Joanne F -- Hopper, John L -- Whiteman, David C -- Pharoah, Paul D -- Easton, Douglas F -- Dunning, Alison M -- Newton-Bishop, Julia A -- Montgomery, Grant W -- Martin, Nicholas G -- Mann, Graham J -- Bishop, D Timothy -- Tsao, Hensin -- Trent, Jeffrey M -- Fisher, David E -- Hayward, Nicholas K -- Brown, Kevin M -- 10118/Cancer Research UK/United Kingdom -- 10589/Cancer Research UK/United Kingdom -- AR043369-14/AR/NIAMS NIH HHS/ -- C490/A11021/Cancer Research UK/United Kingdom -- C588/A10589/Cancer Research UK/United Kingdom -- C588/A4994/Cancer Research UK/United Kingdom -- C8197/A10123/Cancer Research UK/United Kingdom -- C8216/A6129/Cancer Research UK/United Kingdom -- CA88363/CA/NCI NIH HHS/ -- K24CA149202/CA/NCI NIH HHS/ -- P50CA9368/CA/NCI NIH HHS/ -- R01 AR043369/AR/NIAMS NIH HHS/ -- R01 CA-83115-01A2/CA/NCI NIH HHS/ -- R01 CA088363/CA/NCI NIH HHS/ -- R01 CA088363-09/CA/NCI NIH HHS/ -- R01 CA83115/CA/NCI NIH HHS/ -- England -- Nature. 2011 Nov 13;480(7375):99-103. doi: 10.1038/nature10630.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Massachusetts 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22080950" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Aged ; Aged, 80 and over ; Female ; Gene Expression Regulation, Neoplastic ; *Genetic Predisposition to Disease ; Humans ; Male ; Melanoma/*genetics ; Microphthalmia-Associated Transcription Factor/*genetics ; Middle Aged ; *Mutation ; Sumoylation/genetics ; Young Adult
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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    Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-06-11
    Description: The generation of reprogrammed induced pluripotent stem cells (iPSCs) from patients with defined genetic disorders holds the promise of increased understanding of the aetiologies of complex diseases and may also facilitate the development of novel therapeutic interventions. We have generated iPSCs from patients with LEOPARD syndrome (an acronym formed from its main features; that is, lentigines, electrocardiographic abnormalities, ocular hypertelorism, pulmonary valve stenosis, abnormal genitalia, retardation of growth and deafness), an autosomal-dominant developmental disorder belonging to a relatively prevalent class of inherited RAS-mitogen-activated protein kinase signalling diseases, which also includes Noonan syndrome, with pleomorphic effects on several tissues and organ systems. The patient-derived cells have a mutation in the PTPN11 gene, which encodes the SHP2 phosphatase. The iPSCs have been extensively characterized and produce multiple differentiated cell lineages. A major disease phenotype in patients with LEOPARD syndrome is hypertrophic cardiomyopathy. We show that in vitro-derived cardiomyocytes from LEOPARD syndrome iPSCs are larger, have a higher degree of sarcomeric organization and preferential localization of NFATC4 in the nucleus when compared with cardiomyocytes derived from human embryonic stem cells or wild-type iPSCs derived from a healthy brother of one of the LEOPARD syndrome patients. These features correlate with a potential hypertrophic state. We also provide molecular insights into signalling pathways that may promote the disease phenotype.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885001/" 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/PMC2885001/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carvajal-Vergara, Xonia -- Sevilla, Ana -- D'Souza, Sunita L -- Ang, Yen-Sin -- Schaniel, Christoph -- Lee, Dung-Fang -- Yang, Lei -- Kaplan, Aaron D -- Adler, Eric D -- Rozov, Roye -- Ge, Yongchao -- Cohen, Ninette -- Edelmann, Lisa J -- Chang, Betty -- Waghray, Avinash -- Su, Jie -- Pardo, Sherly -- Lichtenbelt, Klaske D -- Tartaglia, Marco -- Gelb, Bruce D -- Lemischka, Ihor R -- 5R01GM078465/GM/NIGMS NIH HHS/ -- R01 GM078465/GM/NIGMS NIH HHS/ -- R01 GM078465-03/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jun 10;465(7299):808-12. doi: 10.1038/nature09005.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York 10029, USA. xcarvajal@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535210" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Cell Differentiation ; Cell Line ; Cell Lineage ; Cells, Cultured ; Embryonic Stem Cells/metabolism ; Enzyme Activation ; Female ; Fibroblasts/metabolism/pathology ; Gene Expression Profiling ; Homeodomain Proteins/genetics ; Humans ; Induced Pluripotent Stem Cells/enzymology/metabolism/*pathology ; LEOPARD Syndrome/drug therapy/metabolism/*pathology ; Male ; Mitogen-Activated Protein Kinases/metabolism ; *Models, Biological ; Myocytes, Cardiac/metabolism/pathology ; NFATC Transcription Factors/genetics/metabolism ; Octamer Transcription Factor-3/genetics ; Phosphoproteins/analysis ; Polymerase Chain Reaction ; *Precision Medicine ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics/metabolism ; SOXB1 Transcription Factors/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Antidiabetic actions of a non-agonist PPARgamma ligand blocking Cdk5-mediated phosphorylation (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-09-06
    Description: PPARgamma is the functioning receptor for the thiazolidinedione (TZD) class of antidiabetes drugs including rosiglitazone and pioglitazone. These drugs are full classical agonists for this nuclear receptor, but recent data have shown that many PPARgamma-based drugs have a separate biochemical activity, blocking the obesity-linked phosphorylation of PPARgamma by Cdk5. Here we describe novel synthetic compounds that have a unique mode of binding to PPARgamma, completely lack classical transcriptional agonism and block the Cdk5-mediated phosphorylation in cultured adipocytes and in insulin-resistant mice. Moreover, one such compound, SR1664, has potent antidiabetic activity while not causing the fluid retention and weight gain that are serious side effects of many of the PPARgamma drugs. Unlike TZDs, SR1664 also does not interfere with bone formation in culture. These data illustrate that new classes of antidiabetes drugs can be developed by specifically targeting the Cdk5-mediated phosphorylation of PPARgamma.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179551/" 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/PMC3179551/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, Jang Hyun -- Banks, Alexander S -- Kamenecka, Theodore M -- Busby, Scott A -- Chalmers, Michael J -- Kumar, Naresh -- Kuruvilla, Dana S -- Shin, Youseung -- He, Yuanjun -- Bruning, John B -- Marciano, David P -- Cameron, Michael D -- Laznik, Dina -- Jurczak, Michael J -- Schurer, Stephan C -- Vidovic, Dusica -- Shulman, Gerald I -- Spiegelman, Bruce M -- Griffin, Patrick R -- 1RC4DK090861/DK/NIDDK NIH HHS/ -- DK31405/DK/NIDDK NIH HHS/ -- R01 DK040936/DK/NIDDK NIH HHS/ -- R01 GM084041/GM/NIGMS NIH HHS/ -- R01 GM084041-03/GM/NIGMS NIH HHS/ -- R01-GM084041/GM/NIGMS NIH HHS/ -- R37 DK031405/DK/NIDDK NIH HHS/ -- R37 DK031405-30/DK/NIDDK NIH HHS/ -- R37 DK031405-31/DK/NIDDK NIH HHS/ -- RC4 DK090861/DK/NIDDK NIH HHS/ -- RC4 DK090861-01/DK/NIDDK NIH HHS/ -- S10 RR027270/RR/NCRR NIH HHS/ -- U24 DK059635/DK/NIDDK NIH HHS/ -- U54 MH074404/MH/NIMH NIH HHS/ -- U54 MH074404-01/MH/NIMH NIH HHS/ -- U54-MH074404/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2011 Sep 4;477(7365):477-81. doi: 10.1038/nature10383.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cancer Biology and Division of Metabolism and Chronic Disease, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21892191" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3-L1 Cells ; Adipocytes/drug effects/metabolism ; Adipose Tissue, White/drug effects/metabolism ; Animals ; Biphenyl Compounds/chemistry/pharmacology ; Body Fluids/drug effects ; COS Cells ; Cercopithecus aethiops ; Cyclin-Dependent Kinase 5/*antagonists & inhibitors ; Dietary Fats/pharmacology ; Disease Models, Animal ; Dose-Response Relationship, Drug ; HEK293 Cells ; Humans ; Hypoglycemic Agents/adverse effects/chemistry/*pharmacology ; Ligands ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Models, Molecular ; Obesity/chemically induced/metabolism ; Osteogenesis/drug effects ; PPAR gamma/agonists/chemistry/*metabolism ; Phosphorylation/drug effects ; Phosphoserine/metabolism ; Thiazolidinediones/adverse effects/pharmacology ; Transcription, Genetic/drug effects ; Tumor Necrosis Factor-alpha/pharmacology ; Weight Gain/drug effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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