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https://www.readbyqxmd.com/read/28541271/protein-altering-and-regulatory-genetic-variants-near-gata4-implicated-in-bicuspid-aortic-valve
#1
Bo Yang, Wei Zhou, Jiao Jiao, Jonas B Nielsen, Michael R Mathis, Mahyar Heydarpour, Guillaume Lettre, Lasse Folkersen, Siddharth Prakash, Claudia Schurmann, Lars Fritsche, Gregory A Farnum, Maoxuan Lin, Mohammad Othman, Whitney Hornsby, Anisa Driscoll, Alexandra Levasseur, Marc Thomas, Linda Farhat, Marie-Pierre Dubé, Eric M Isselbacher, Anders Franco-Cereceda, Dong-Chuan Guo, Erwin P Bottinger, G Michael Deeb, Anna Booher, Sachin Kheterpal, Y Eugene Chen, Hyun Min Kang, Jacob Kitzman, Heather J Cordell, Bernard D Keavney, Judith A Goodship, Santhi K Ganesh, Gonçalo Abecasis, Kim A Eagle, Alan P Boyle, Ruth J F Loos, Per Eriksson, Jean-Claude Tardif, Chad M Brummett, Dianna M Milewicz, Simon C Body, Cristen J Willer
Bicuspid aortic valve (BAV) is a heritable congenital heart defect and an important risk factor for valvulopathy and aortopathy. Here we report a genome-wide association scan of 466 BAV cases and 4,660 age, sex and ethnicity-matched controls with replication in up to 1,326 cases and 8,103 controls. We identify association with a noncoding variant 151 kb from the gene encoding the cardiac-specific transcription factor, GATA4, and near-significance for p.Ser377Gly in GATA4. GATA4 was interrupted by CRISPR-Cas9 in induced pluripotent stem cells from healthy donors...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28537254/large-scale-meta-analysis-characterizes-genetic-architecture-for-common-psoriasis-associated-variants
#2
Lam C Tsoi, Philip E Stuart, Chao Tian, Johann E Gudjonsson, Sayantan Das, Matthew Zawistowski, Eva Ellinghaus, Jonathan N Barker, Vinod Chandran, Nick Dand, Kristina Callis Duffin, Charlotta Enerbäck, Tõnu Esko, Andre Franke, Dafna D Gladman, Per Hoffmann, Külli Kingo, Sulev Kõks, Gerald G Krueger, Henry W Lim, Andres Metspalu, Ulrich Mrowietz, Sören Mucha, Proton Rahman, Andre Reis, Trilokraj Tejasvi, Richard Trembath, John J Voorhees, Stephan Weidinger, Michael Weichenthal, Xiaoquan Wen, Nicholas Eriksson, Hyun M Kang, David A Hinds, Rajan P Nair, Gonçalo R Abecasis, James T Elder
Psoriasis is a complex disease of skin with a prevalence of about 2%. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for psoriasis to date, including data from eight different Caucasian cohorts, with a combined effective sample size >39,000 individuals. We identified 16 additional psoriasis susceptibility loci achieving genome-wide significance, increasing the number of identified loci to 63 for European-origin individuals. Functional analysis highlighted the roles of interferon signalling and the NFκB cascade, and we showed that the psoriasis signals are enriched in regulatory elements from different T cells (CD8(+) T-cells and CD4(+) T-cells including TH0, TH1 and TH17)...
May 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28506971/protein-truncating-variants-at-the-cholesteryl-ester-transfer-protein-gene-and-risk-for-coronary-heart-disease
#3
Akihiro Nomura, Hong-Hee Won, Amit V Khera, Fumihiko Takeuchi, Kaoru Ito, Shane McCarthy, Connor A Emdin, Derek Klarin, Pradeep Natarajan, Seyedeh M Zekavat, Namrata Gupta, Gina M Peloso, Ingrid B Borecki, Tanya M Teslovich, Rosanna Asselta, Stefano Duga, Piera A Merlini, Adolfo Correa, Thorsten Kessler, James G Wilson, Matthew J Bown, Alistair S Hall, Peter S Braund, David J Carey, Michael F Murray, H L Kirchner, Joseph B Leader, Daniel R Lavage, J N Manus, Dustin N Hartzel, Nilesh J Samani, Heribert Schunkert, Jaume Marrugat, Roberto Elosua, Ruth McPherson, Martin Farrall, Hugh Watkins, Jyh-Ming Jimmy Juang, Chao A Hsiung, Shih-Yi Lin, Jun-Sing Wang, Hayato Tada, Masa-Aki Kawashiri, Akihiro Inazu, Masakazu Yamagishi, Tomohiro Katsuya, Eitaro Nakashima, Masahiro Nakatochi, Ken Yamamoto, Mitsuhiro Yokota, Yukihide Momozawa, Jerome I Rotter, Eric S Lander, Daniel J Rader, John N Danesh, Diego Ardissino, Stacey B Gabriel, Cristen J Willer, Gonçalo Abecasis, Danish Saleheen, Michiaki Kubo, Norihiro Kato, Yii-Der I Chen, Frederick Dewey, Sekar Kathiresan
Rationale: Therapies which inhibit cholesteryl ester transfer protein (CETP) have failed to demonstrate a reduction in risk for coronary heart disease (CHD). Human deoxyribonucleic acid sequence variants that truncate the CETP gene may provide insight into the efficacy of CETP inhibition. Objective: To test whether protein truncating variants (PTVs) at the CETP gene were associated with plasma lipid levels and CHD. Methods and Results: We sequenced the exons of the CETP gene in 58,469 participants from 12 case-control studies (18,817 CHD cases, 39,652 CHD-free controls)...
May 15, 2017: Circulation Research
https://www.readbyqxmd.com/read/28453676/fastmitocalc-an-ultra-fast-program-to-estimate-mitochondrial-dna-copy-number-from-whole-genome-sequences
#4
Yong Qian, Thomas J Butler, Krista Opsahl-Ong, Nicholas S Giroux, Carlo Sidore, Ramaiah Nagaraja, Francesco Cucca, Luigi Ferrucci, Gonçalo R Abecasis, David Schlessinger, Jun Ding
Availability and Implementation: fastMitoCalc is available at https://lgsun.irp.nia.nih.gov/hsgu/software/mitoAnalyzer/index.html. Contact: jun.ding@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online.
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28448500/genome-wide-physical-activity-interactions-in-adiposity-a-meta-analysis-of-200-452-adults
#5
Mariaelisa Graff, Robert A Scott, Anne E Justice, Kristin L Young, Mary F Feitosa, Llilda Barata, Thomas W Winkler, Audrey Y Chu, Anubha Mahajan, David Hadley, Luting Xue, Tsegaselassie Workalemahu, Nancy L Heard-Costa, Marcel den Hoed, Tarunveer S Ahluwalia, Qibin Qi, Julius S Ngwa, Frida Renström, Lydia Quaye, John D Eicher, James E Hayes, Marilyn Cornelis, Zoltan Kutalik, Elise Lim, Jian'an Luan, Jennifer E Huffman, Weihua Zhang, Wei Zhao, Paula J Griffin, Toomas Haller, Shafqat Ahmad, Pedro M Marques-Vidal, Stephanie Bien, Loic Yengo, Alexander Teumer, Albert Vernon Smith, Meena Kumari, Marie Neergaard Harder, Johanne Marie Justesen, Marcus E Kleber, Mette Hollensted, Kurt Lohman, Natalia V Rivera, John B Whitfield, Jing Hua Zhao, Heather M Stringham, Leo-Pekka Lyytikäinen, Charlotte Huppertz, Gonneke Willemsen, Wouter J Peyrot, Ying Wu, Kati Kristiansson, Ayse Demirkan, Myriam Fornage, Maija Hassinen, Lawrence F Bielak, Gemma Cadby, Toshiko Tanaka, Reedik Mägi, Peter J van der Most, Anne U Jackson, Jennifer L Bragg-Gresham, Veronique Vitart, Jonathan Marten, Pau Navarro, Claire Bellis, Dorota Pasko, Åsa Johansson, Søren Snitker, Yu-Ching Cheng, Joel Eriksson, Unhee Lim, Mette Aadahl, Linda S Adair, Najaf Amin, Beverley Balkau, Juha Auvinen, John Beilby, Richard N Bergman, Sven Bergmann, Alain G Bertoni, John Blangero, Amélie Bonnefond, Lori L Bonnycastle, Judith B Borja, Søren Brage, Fabio Busonero, Steve Buyske, Harry Campbell, Peter S Chines, Francis S Collins, Tanguy Corre, George Davey Smith, Graciela E Delgado, Nicole Dueker, Marcus Dörr, Tapani Ebeling, Gudny Eiriksdottir, Tõnu Esko, Jessica D Faul, Mao Fu, Kristine Færch, Christian Gieger, Sven Gläser, Jian Gong, Penny Gordon-Larsen, Harald Grallert, Tanja B Grammer, Niels Grarup, Gerard van Grootheest, Kennet Harald, Nicholas D Hastie, Aki S Havulinna, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Oddgeir L Holmens, Christina Holzapfel, Jouke Jan Hottenga, Jie Huang, Tao Huang, Jennie Hui, Cornelia Huth, Nina Hutri-Kähönen, Alan L James, John-Olov Jansson, Min A Jhun, Markus Juonala, Leena Kinnunen, Heikki A Koistinen, Ivana Kolcic, Pirjo Komulainen, Johanna Kuusisto, Kirsti Kvaløy, Mika Kähönen, Timo A Lakka, Lenore J Launer, Benjamin Lehne, Cecilia M Lindgren, Mattias Lorentzon, Robert Luben, Michel Marre, Yuri Milaneschi, Keri L Monda, Grant W Montgomery, Marleen H M De Moor, Antonella Mulas, Martina Müller-Nurasyid, A W Musk, Reija Männikkö, Satu Männistö, Narisu Narisu, Matthias Nauck, Jennifer A Nettleton, Ilja M Nolte, Albertine J Oldehinkel, Matthias Olden, Ken K Ong, Sandosh Padmanabhan, Lavinia Paternoster, Jeremiah Perez, Markus Perola, Annette Peters, Ulrike Peters, Patricia A Peyser, Inga Prokopenko, Hannu Puolijoki, Olli T Raitakari, Tuomo Rankinen, Laura J Rasmussen-Torvik, Rajesh Rawal, Paul M Ridker, Lynda M Rose, Igor Rudan, Cinzia Sarti, Mark A Sarzynski, Kai Savonen, William R Scott, Serena Sanna, Alan R Shuldiner, Steve Sidney, Günther Silbernagel, Blair H Smith, Jennifer A Smith, Harold Snieder, Alena Stančáková, Barbara Sternfeld, Amy J Swift, Tuija Tammelin, Sian-Tsung Tan, Barbara Thorand, Dorothée Thuillier, Liesbeth Vandenput, Henrik Vestergaard, Jana V van Vliet-Ostaptchouk, Marie-Claude Vohl, Uwe Völker, Gérard Waeber, Mark Walker, Sarah Wild, Andrew Wong, Alan F Wright, M Carola Zillikens, Niha Zubair, Christopher A Haiman, Loic Lemarchand, Ulf Gyllensten, Claes Ohlsson, Albert Hofman, Fernando Rivadeneira, André G Uitterlinden, Louis Pérusse, James F Wilson, Caroline Hayward, Ozren Polasek, Francesco Cucca, Kristian Hveem, Catharina A Hartman, Anke Tönjes, Stefania Bandinelli, Lyle J Palmer, Sharon L R Kardia, Rainer Rauramaa, Thorkild I A Sørensen, Jaakko Tuomilehto, Veikko Salomaa, Brenda W J H Penninx, Eco J C de Geus, Dorret I Boomsma, Terho Lehtimäki, Massimo Mangino, Markku Laakso, Claude Bouchard, Nicholas G Martin, Diana Kuh, Yongmei Liu, Allan Linneberg, Winfried März, Konstantin Strauch, Mika Kivimäki, Tamara B Harris, Vilmundur Gudnason, Henry Völzke, Lu Qi, Marjo-Riitta Järvelin, John C Chambers, Jaspal S Kooner, Philippe Froguel, Charles Kooperberg, Peter Vollenweider, Göran Hallmans, Torben Hansen, Oluf Pedersen, Andres Metspalu, Nicholas J Wareham, Claudia Langenberg, David R Weir, David J Porteous, Eric Boerwinkle, Daniel I Chasman, Gonçalo R Abecasis, Inês Barroso, Mark I McCarthy, Timothy M Frayling, Jeffrey R O'Connell, Cornelia M van Duijn, Michael Boehnke, Iris M Heid, Karen L Mohlke, David P Strachan, Caroline S Fox, Ching-Ti Liu, Joel N Hirschhorn, Robert J Klein, Andrew D Johnson, Ingrid B Borecki, Paul W Franks, Kari E North, L Adrienne Cupples, Ruth J F Loos, Tuomas O Kilpeläinen
Physical activity (PA) may modify the genetic effects that give rise to increased risk of obesity. To identify adiposity loci whose effects are modified by PA, we performed genome-wide interaction meta-analyses of BMI and BMI-adjusted waist circumference and waist-hip ratio from up to 200,452 adults of European (n = 180,423) or other ancestry (n = 20,029). We standardized PA by categorizing it into a dichotomous variable where, on average, 23% of participants were categorized as inactive and 77% as physically active...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28445677/overexpression-of-the-cytokine-baff-and-autoimmunity-risk
#6
Maristella Steri, Valeria Orrù, M Laura Idda, Maristella Pitzalis, Mauro Pala, Ilenia Zara, Carlo Sidore, Valeria Faà, Matteo Floris, Manila Deiana, Isadora Asunis, Eleonora Porcu, Antonella Mulas, Maria G Piras, Monia Lobina, Sandra Lai, Mara Marongiu, Valentina Serra, Michele Marongiu, Gabriella Sole, Fabio Busonero, Andrea Maschio, Roberto Cusano, Gianmauro Cuccuru, Francesca Deidda, Fausto Poddie, Gabriele Farina, Mariano Dei, Francesca Virdis, Stefania Olla, Maria A Satta, Mario Pani, Alessandro Delitala, Eleonora Cocco, Jessica Frau, Giancarlo Coghe, Lorena Lorefice, Giuseppe Fenu, Paola Ferrigno, Maria Ban, Nadia Barizzone, Maurizio Leone, Franca R Guerini, Matteo Piga, Davide Firinu, Ingrid Kockum, Izaura Lima Bomfim, Tomas Olsson, Lars Alfredsson, Ana Suarez, Patricia E Carreira, Maria J Castillo-Palma, Joseph H Marcus, Mauro Congia, Andrea Angius, Maurizio Melis, Antonio Gonzalez, Marta E Alarcón Riquelme, Berta M da Silva, Maurizio Marchini, Maria G Danieli, Stefano Del Giacco, Alessandro Mathieu, Antonello Pani, Stephen B Montgomery, Giulio Rosati, Jan Hillert, Stephen Sawcer, Sandra D'Alfonso, John A Todd, John Novembre, Gonçalo R Abecasis, Michael B Whalen, Maria G Marrosu, Alessandra Meloni, Serena Sanna, Myriam Gorospe, David Schlessinger, Edoardo Fiorillo, Magdalena Zoledziewska, Francesco Cucca
BACKGROUND: Genomewide association studies of autoimmune diseases have mapped hundreds of susceptibility regions in the genome. However, only for a few association signals has the causal gene been identified, and for even fewer have the causal variant and underlying mechanism been defined. Coincident associations of DNA variants affecting both the risk of autoimmune disease and quantitative immune variables provide an informative route to explore disease mechanisms and drug-targetable pathways...
April 27, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28443625/genome-wide-meta-analysis-of-241-258-adults-accounting-for-smoking-behaviour-identifies-novel-loci-for-obesity-traits
#7
Anne E Justice, Thomas W Winkler, Mary F Feitosa, Misa Graff, Virginia A Fisher, Kristin Young, Llilda Barata, Xuan Deng, Jacek Czajkowski, David Hadley, Julius S Ngwa, Tarunveer S Ahluwalia, Audrey Y Chu, Nancy L Heard-Costa, Elise Lim, Jeremiah Perez, John D Eicher, Zoltán Kutalik, Luting Xue, Anubha Mahajan, Frida Renström, Joseph Wu, Qibin Qi, Shafqat Ahmad, Tamuno Alfred, Najaf Amin, Lawrence F Bielak, Amelie Bonnefond, Jennifer Bragg, Gemma Cadby, Martina Chittani, Scott Coggeshall, Tanguy Corre, Nese Direk, Joel Eriksson, Krista Fischer, Mathias Gorski, Marie Neergaard Harder, Momoko Horikoshi, Tao Huang, Jennifer E Huffman, Anne U Jackson, Johanne Marie Justesen, Stavroula Kanoni, Leena Kinnunen, Marcus E Kleber, Pirjo Komulainen, Meena Kumari, Unhee Lim, Jian'an Luan, Leo-Pekka Lyytikäinen, Massimo Mangino, Ani Manichaikul, Jonathan Marten, Rita P S Middelberg, Martina Müller-Nurasyid, Pau Navarro, Louis Pérusse, Natalia Pervjakova, Cinzia Sarti, Albert Vernon Smith, Jennifer A Smith, Alena Stančáková, Rona J Strawbridge, Heather M Stringham, Yun Ju Sung, Toshiko Tanaka, Alexander Teumer, Stella Trompet, Sander W van der Laan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Sailaja L Vedantam, Niek Verweij, Jacqueline M Vink, Veronique Vitart, Ying Wu, Loic Yengo, Weihua Zhang, Jing Hua Zhao, Martina E Zimmermann, Niha Zubair, Gonçalo R Abecasis, Linda S Adair, Saima Afaq, Uzma Afzal, Stephan J L Bakker, Traci M Bartz, John Beilby, Richard N Bergman, Sven Bergmann, Reiner Biffar, John Blangero, Eric Boerwinkle, Lori L Bonnycastle, Erwin Bottinger, Daniele Braga, Brendan M Buckley, Steve Buyske, Harry Campbell, John C Chambers, Francis S Collins, Joanne E Curran, Gert J de Borst, Anton J M de Craen, Eco J C de Geus, George Dedoussis, Graciela E Delgado, Hester M den Ruijter, Gudny Eiriksdottir, Anna L Eriksson, Tõnu Esko, Jessica D Faul, Ian Ford, Terrence Forrester, Karl Gertow, Bruna Gigante, Nicola Glorioso, Jian Gong, Harald Grallert, Tanja B Grammer, Niels Grarup, Saskia Haitjema, Göran Hallmans, Anders Hamsten, Torben Hansen, Tamara B Harris, Catharina A Hartman, Maija Hassinen, Nicholas D Hastie, Andrew C Heath, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, Georg Homuth, Jouke Jan Hottenga, Jie Huang, Joseph Hung, Nina Hutri-Kähönen, Erik Ingelsson, Alan L James, John-Olov Jansson, Marjo-Riitta Jarvelin, Min A Jhun, Marit E Jørgensen, Markus Juonala, Mika Kähönen, Magnus Karlsson, Heikki A Koistinen, Ivana Kolcic, Genovefa Kolovou, Charles Kooperberg, Bernhard K Krämer, Johanna Kuusisto, Kirsti Kvaløy, Timo A Lakka, Claudia Langenberg, Lenore J Launer, Karin Leander, Nanette R Lee, Lars Lind, Cecilia M Lindgren, Allan Linneberg, Stephane Lobbens, Marie Loh, Mattias Lorentzon, Robert Luben, Gitta Lubke, Anja Ludolph-Donislawski, Sara Lupoli, Pamela A F Madden, Reija Männikkö, Pedro Marques-Vidal, Nicholas G Martin, Colin A McKenzie, Barbara McKnight, Dan Mellström, Cristina Menni, Grant W Montgomery, Aw Bill Musk, Narisu Narisu, Matthias Nauck, Ilja M Nolte, Albertine J Oldehinkel, Matthias Olden, Ken K Ong, Sandosh Padmanabhan, Patricia A Peyser, Charlotta Pisinger, David J Porteous, Olli T Raitakari, Tuomo Rankinen, D C Rao, Laura J Rasmussen-Torvik, Rajesh Rawal, Treva Rice, Paul M Ridker, Lynda M Rose, Stephanie A Bien, Igor Rudan, Serena Sanna, Mark A Sarzynski, Naveed Sattar, Kai Savonen, David Schlessinger, Salome Scholtens, Claudia Schurmann, Robert A Scott, Bengt Sennblad, Marten A Siemelink, Günther Silbernagel, P Eline Slagboom, Harold Snieder, Jan A Staessen, David J Stott, Morris A Swertz, Amy J Swift, Kent D Taylor, Bamidele O Tayo, Barbara Thorand, Dorothee Thuillier, Jaakko Tuomilehto, Andre G Uitterlinden, Liesbeth Vandenput, Marie-Claude Vohl, Henry Völzke, Judith M Vonk, Gérard Waeber, Melanie Waldenberger, R G J Westendorp, Sarah Wild, Gonneke Willemsen, Bruce H R Wolffenbuttel, Andrew Wong, Alan F Wright, Wei Zhao, M Carola Zillikens, Damiano Baldassarre, Beverley Balkau, Stefania Bandinelli, Carsten A Böger, Dorret I Boomsma, Claude Bouchard, Marcel Bruinenberg, Daniel I Chasman, Yii-DerIda Chen, Peter S Chines, Richard S Cooper, Francesco Cucca, Daniele Cusi, Ulf de Faire, Luigi Ferrucci, Paul W Franks, Philippe Froguel, Penny Gordon-Larsen, Hans-Jörgen Grabe, Vilmundur Gudnason, Christopher A Haiman, Caroline Hayward, Kristian Hveem, Andrew D Johnson, J Wouter Jukema, Sharon L R Kardia, Mika Kivimaki, Jaspal S Kooner, Diana Kuh, Markku Laakso, Terho Lehtimäki, Loic Le Marchand, Winfried März, Mark I McCarthy, Andres Metspalu, Andrew P Morris, Claes Ohlsson, Lyle J Palmer, Gerard Pasterkamp, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, Bruce M Psaty, Lu Qi, Rainer Rauramaa, Blair H Smith, Thorkild I A Sørensen, Konstantin Strauch, Henning Tiemeier, Elena Tremoli, Pim van der Harst, Henrik Vestergaard, Peter Vollenweider, Nicholas J Wareham, David R Weir, John B Whitfield, James F Wilson, Jessica Tyrrell, Timothy M Frayling, Inês Barroso, Michael Boehnke, Panagiotis Deloukas, Caroline S Fox, Joel N Hirschhorn, David J Hunter, Tim D Spector, David P Strachan, Cornelia M van Duijn, Iris M Heid, Karen L Mohlke, Jonathan Marchini, Ruth J F Loos, Tuomas O Kilpeläinen, Ching-Ti Liu, Ingrid B Borecki, Kari E North, L Adrienne Cupples
Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28429804/identifying-tagging-snps-for-african-specific-genetic-variation-from-the-african-diaspora-genome
#8
Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timothy D O'Connor, Gonçalo R Abecasis, Genevieve L Wojcik, Christopher R Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E Kenny, Carlos Bustamante, Terri H Beaty, Rasika A Mathias, Kathleen C Barnes, Zhaohui S Qin
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28394350/population-and-individual-specific-regulatory-variation-in-sardinia
#9
Mauro Pala, Zachary Zappala, Mara Marongiu, Xin Li, Joe R Davis, Roberto Cusano, Francesca Crobu, Kimberly R Kukurba, Michael J Gloudemans, Frederic Reinier, Riccardo Berutti, Maria G Piras, Antonella Mulas, Magdalena Zoledziewska, Michele Marongiu, Elena P Sorokin, Gaelen T Hess, Kevin S Smith, Fabio Busonero, Andrea Maschio, Maristella Steri, Carlo Sidore, Serena Sanna, Edoardo Fiorillo, Michael C Bassik, Stephen J Sawcer, Alexis Battle, John Novembre, Chris Jones, Andrea Angius, Gonçalo R Abecasis, David Schlessinger, Francesco Cucca, Stephen B Montgomery
Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicing. We identified 21,183 expression quantitative trait loci (eQTLs) and 6,768 splicing quantitative trait loci (sQTLs), including 619 new QTLs. We identified high-frequency QTLs and found evidence of selection near genes involved in malarial resistance and increased multiple sclerosis risk, reflecting the epidemiological history of Sardinia...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/28341696/a-low-frequency-inactivating-akt2-variant-enriched-in-the-finnish-population-is-associated-with-fasting-insulin-levels-and-type-2-diabetes-risk
#10
Alisa Manning, Heather M Highland, Jessica Gasser, Xueling Sim, Taru Tukiainen, Pierre Fontanillas, Niels Grarup, Manuel A Rivas, Anubha Mahajan, Adam E Locke, Pablo Cingolani, Tune H Pers, Ana Viñuela, Andrew A Brown, Ying Wu, Jason Flannick, Christian Fuchsberger, Eric R Gamazon, Kyle J Gaulton, Hae Kyung Im, Tanya M Teslovich, Thomas W Blackwell, Jette Bork-Jensen, Noël P Burtt, Yuhui Chen, Todd Green, Christopher Hartl, Hyun Min Kang, Ashish Kumar, Claes Ladenvall, Clement Ma, Loukas Moutsianas, Richard D Pearson, John R B Perry, N William Rayner, Neil R Robertson, Laura J Scott, Martijn van de Bunt, Johan G Eriksson, Antti Jula, Seppo Koskinen, Terho Lehtimäki, Aarno Palotie, Olli T Raitakari, Suzanne Br Jacobs, Jennifer Wessel, Audrey Y Chu, Robert A Scott, Mark O Goodarzi, Christine Blancher, Gemma Buck, David Buck, Peter S Chines, Stacey Gabriel, Anette P Gjesing, Christopher J Groves, Mette Hollensted, Jeroen R Huyghe, Anne U Jackson, Goo Jun, Johanne Marie Justesen, Massimo Mangino, Jacquelyn Murphy, Matt Neville, Robert Onofrio, Kerrin S Small, Heather M Stringham, Joseph Trakalo, Eric Banks, Jason Carey, Mauricio O Carneiro, Mark DePristo, Yossi Farjoun, Timothy Fennell, Jacqueline I Goldstein, George Grant, Martin Hrabé de Angelis, Jared Maguire, Benjamin M Neale, Ryan Poplin, Shaun Purcell, Thomas Schwarzmayr, Khalid Shakir, Joshua D Smith, Tim M Strom, Thomas Wieland, Jaana Lindstrom, Ivan Brandslund, Cramer Christensen, Gabriela L Surdulescu, Timo A Lakka, Alex S F Doney, Peter Nilsson, Nicholas J Wareham, Claudia Langenberg, Tibor V Varga, Paul W Franks, Olov Rolandsson, Anders H Rosengren, Vidya S Farook, Farook Thameem, Sobha Puppala, Satish Kumar, Donna M Lehman, Christopher P Jenkinson, Joanne E Curran, Daniel Esten Hale, Sharon P Fowler, Rector Arya, Ralph A DeFronzo, Hanna E Abboud, Ann-Christine Syvänen, Pamela J Hicks, Nicholette D Palmer, Maggie C Y Ng, Donald W Bowden, Barry I Freedman, Tõnu Esko, Reedik Mägi, Lili Milani, Evelin Mihailov, Andres Metspalu, Narisu Narisu, Leena Kinnunen, Lori L Bonnycastle, Amy Swift, Dorota Pasko, Andrew R Wood, João Fadista, Toni I Pollin, Nir Barzilai, Gil Atzmon, Benjamin Glaser, Barbara Thorand, Konstantin Strauch, Annette Peters, Michael Roden, Martina Müller-Nurasyid, Liming Liang, Jennifer Kriebel, Thomas Illig, Harald Grallert, Christian Gieger, Christa Meisinger, Lars Lannfelt, Solomon K Musani, Michael Griswold, Herman A Taylor, Gregory Wilson, Adolfo Correa, Heikki Oksa, William R Scott, Uzma Afzal, Sian-Tsung Tan, Marie Loh, John C Chambers, Jobanpreet Sehmi, Jaspal Singh Kooner, Benjamin Lehne, Yoon Shin Cho, Jong-Young Lee, Bok-Ghee Han, Annemari Käräjämäki, Qibin Qi, Lu Qi, Jinyan Huang, Frank B Hu, Olle Melander, Marju Orho-Melander, Jennifer E Below, David Aguilar, Tien Yin Wong, Jianjun Liu, Chiea-Chuen Khor, Kee Seng Chia, Wei Yen Lim, Ching-Yu Cheng, Edmund Chan, E Shyong Tai, Tin Aung, Allan Linneberg, Bo Isomaa, Thomas Meitinger, Tiinamaija Tuomi, Liisa Hakaste, Jasmina Kravic, Marit E Jørgensen, Torsten Lauritzen, Panos Deloukas, Kathleen E Stirrups, Katharine R Owen, Andrew J Farmer, Timothy M Frayling, Stephen P O'Rahilly, Mark Walker, Jonathan C Levy, Dylan Hodgkiss, Andrew T Hattersley, Teemu Kuulasmaa, Alena Stančáková, Inês Barroso, Dwaipayan Bharadwaj, Juliana Chan, Giriraj R Chandak, Mark J Daly, Peter J Donnelly, Shah B Ebrahim, Paul Elliott, Tasha Fingerlin, Philippe Froguel, Cheng Hu, Weiping Jia, Ronald C W Ma, Gilean McVean, Taesung Park, Dorairaj Prabhakaran, Manjinder Sandhu, James Scott, Rob Sladek, Nikhil Tandon, Yik Ying Teo, Eleftheria Zeggini, Richard M Watanabe, Heikki A Koistinen, Y Antero Kesaniemi, Matti Uusitupa, Timothy D Spector, Veikko Salomaa, Rainer Rauramaa, Colin N A Palmer, Inga Prokopenko, Andrew D Morris, Richard N Bergman, Francis S Collins, Lars Lind, Erik Ingelsson, Jaakko Tuomilehto, Fredrik Karpe, Leif Groop, Torben Jørgensen, Torben Hansen, Oluf Pedersen, Johanna Kuusisto, Gonçalo Abecasis, Graeme I Bell, John Blangero, Nancy J Cox, Ravindranath Duggirala, Mark Seielstad, James G Wilson, Josee Dupuis, Samuli Ripatti, Craig L Hanis, Jose C Florez, Karen L Mohlke, James B Meigs, Markku Laakso, Andrew P Morris, Michael Boehnke, David Altshuler, Mark I McCarthy, Anna L Gloyn, Cecilia M Lindgren
To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting insulin, a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders...
March 24, 2017: Diabetes
https://www.readbyqxmd.com/read/28341650/bivariate-analysis-of-age-related-macular-degeneration-progression-using-genetic-risk-scores
#11
Ying Ding, Yi Liu, Qi Yan, Lars G Fritsche, Richard J Cook, Traci Clemons, Rinki Ratnapriya, Michael L Klein, Gonçalo R Abecasis, Anand Swaroop, Emily Y Chew, Daniel E Weeks, Wei Chen
Age-related macular degeneration (AMD) is a leading cause of blindness in the developed world. While many AMD susceptibility variants have been identified, their influence on AMD progression has not been elucidated. Using data from two large clinical trials, Age-Related Eye Disease Study (AREDS) and AREDS2, we evaluated the effects of 34 known risk variants on disease progression. In doing so, we calculated the eye-level time-to-late AMD and modeled them using a bivariate survival analysis approach, appropriately accounting for between-eye correlation...
May 2017: Genetics
https://www.readbyqxmd.com/read/28267856/association-of-rare-and-common-variation-in-the-lipoprotein-lipase-gene-with-coronary-artery-disease
#12
Amit V Khera, Hong-Hee Won, Gina M Peloso, Colm O'Dushlaine, Dajiang Liu, Nathan O Stitziel, Pradeep Natarajan, Akihiro Nomura, Connor A Emdin, Namrata Gupta, Ingrid B Borecki, Rosanna Asselta, Stefano Duga, Piera Angelica Merlini, Adolfo Correa, Thorsten Kessler, James G Wilson, Matthew J Bown, Alistair S Hall, Peter S Braund, David J Carey, Michael F Murray, H Lester Kirchner, Joseph B Leader, Daniel R Lavage, J Neil Manus, Dustin N Hartzel, Nilesh J Samani, Heribert Schunkert, Jaume Marrugat, Roberto Elosua, Ruth McPherson, Martin Farrall, Hugh Watkins, Eric S Lander, Daniel J Rader, John Danesh, Diego Ardissino, Stacey Gabriel, Cristen Willer, Gonçalo R Abecasis, Danish Saleheen, Frederick E Dewey, Sekar Kathiresan
Importance: The activity of lipoprotein lipase (LPL) is the rate-determining step in clearing triglyceride-rich lipoproteins from the circulation. Mutations that damage the LPL gene (LPL) lead to lifelong deficiency in enzymatic activity and can provide insight into the relationship of LPL to human disease. Objective: To determine whether rare and/or common variants in LPL are associated with early-onset coronary artery disease (CAD). Design, Setting, and Participants: In a cross-sectional study, LPL was sequenced in 10 CAD case-control cohorts of the multinational Myocardial Infarction Genetics Consortium and a nested CAD case-control cohort of the Geisinger Health System DiscovEHR cohort between 2010 and 2015...
March 7, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28241208/association-between-telomere-length-and-risk-of-cancer-and-non-neoplastic-diseases-a-mendelian-randomization-study
#13
Philip C Haycock, Stephen Burgess, Aayah Nounu, Jie Zheng, George N Okoli, Jack Bowden, Kaitlin Hazel Wade, Nicholas J Timpson, David M Evans, Peter Willeit, Abraham Aviv, Tom R Gaunt, Gibran Hemani, Massimo Mangino, Hayley Patricia Ellis, Kathreena M Kurian, Karen A Pooley, Rosalind A Eeles, Jeffrey E Lee, Shenying Fang, Wei V Chen, Matthew H Law, Lisa M Bowdler, Mark M Iles, Qiong Yang, Bradford B Worrall, Hugh Stephen Markus, Rayjean J Hung, Chris I Amos, Amanda B Spurdle, Deborah J Thompson, Tracy A O'Mara, Brian Wolpin, Laufey Amundadottir, Rachael Stolzenberg-Solomon, Antonia Trichopoulou, N Charlotte Onland-Moret, Eiliv Lund, Eric J Duell, Federico Canzian, Gianluca Severi, Kim Overvad, Marc J Gunter, Rosario Tumino, Ulrika Svenson, Andre van Rij, Annette F Baas, Matthew J Bown, Nilesh J Samani, Femke N G van t'Hof, Gerard Tromp, Gregory T Jones, Helena Kuivaniemi, James R Elmore, Mattias Johansson, James Mckay, Ghislaine Scelo, Robert Carreras-Torres, Valerie Gaborieau, Paul Brennan, Paige M Bracci, Rachel E Neale, Sara H Olson, Steven Gallinger, Donghui Li, Gloria M Petersen, Harvey A Risch, Alison P Klein, Jiali Han, Christian C Abnet, Neal D Freedman, Philip R Taylor, John M Maris, Katja K Aben, Lambertus A Kiemeney, Sita H Vermeulen, John K Wiencke, Kyle M Walsh, Margaret Wrensch, Terri Rice, Clare Turnbull, Kevin Litchfield, Lavinia Paternoster, Marie Standl, Gonçalo R Abecasis, John Paul SanGiovanni, Yong Li, Vladan Mijatovic, Yadav Sapkota, Siew-Kee Low, Krina T Zondervan, Grant W Montgomery, Dale R Nyholt, David A van Heel, Karen Hunt, Dan E Arking, Foram N Ashar, Nona Sotoodehnia, Daniel Woo, Jonathan Rosand, Mary E Comeau, W Mark Brown, Edwin K Silverman, John E Hokanson, Michael H Cho, Jennie Hui, Manuel A Ferreira, Philip J Thompson, Alanna C Morrison, Janine F Felix, Nicholas L Smith, Angela M Christiano, Lynn Petukhova, Regina C Betz, Xing Fan, Xuejun Zhang, Caihong Zhu, Carl D Langefeld, Susan D Thompson, Feijie Wang, Xu Lin, David A Schwartz, Tasha Fingerlin, Jerome I Rotter, Mary Frances Cotch, Richard A Jensen, Matthias Munz, Henrik Dommisch, Arne S Schaefer, Fang Han, Hanna M Ollila, Ryan P Hillary, Omar Albagha, Stuart H Ralston, Chenjie Zeng, Wei Zheng, Xiao-Ou Shu, Andre Reis, Steffen Uebe, Ulrike Hüffmeier, Yoshiya Kawamura, Takeshi Otowa, Tsukasa Sasaki, Martin Lloyd Hibberd, Sonia Davila, Gang Xie, Katherine Siminovitch, Jin-Xin Bei, Yi-Xin Zeng, Asta Försti, Bowang Chen, Stefano Landi, Andre Franke, Annegret Fischer, David Ellinghaus, Carlos Flores, Imre Noth, Shwu-Fan Ma, Jia Nee Foo, Jianjun Liu, Jong-Won Kim, David G Cox, Olivier Delattre, Olivier Mirabeau, Christine F Skibola, Clara S Tang, Merce Garcia-Barcelo, Kai-Ping Chang, Wen-Hui Su, Yu-Sun Chang, Nicholas G Martin, Scott Gordon, Tracey D Wade, Chaeyoung Lee, Michiaki Kubo, Pei-Chieng Cha, Yusuke Nakamura, Daniel Levy, Masayuki Kimura, Shih-Jen Hwang, Steven Hunt, Tim Spector, Nicole Soranzo, Ani W Manichaikul, R Graham Barr, Bratati Kahali, Elizabeth Speliotes, Laura M Yerges-Armstrong, Ching-Yu Cheng, Jost B Jonas, Tien Yin Wong, Isabella Fogh, Kuang Lin, John F Powell, Kenneth Rice, Caroline L Relton, Richard M Martin, George Davey Smith
Importance: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. Objective: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. Data Sources: Genomewide association studies (GWAS) published up to January 15, 2015...
May 1, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28200055/laser-server-ancestry-tracing-with-genotypes-or-sequence-reads
#14
Daniel Taliun, Sonia Chothani, Sebastian Schönherr, Lukas Forer, Michael Boehnke, Gonçalo R Abecasis, Chaolong Wang
No abstract text is available yet for this article.
February 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28177087/mitogenome-diversity-in-sardinians-a-genetic-window-onto-an-island-s-past
#15
Anna Olivieri, Carlo Sidore, Alessandro Achilli, Andrea Angius, Cosimo Posth, Anja Furtwängler, Stefania Brandini, Marco Rosario Capodiferro, Francesca Gandini, Magdalena Zoledziewska, Maristella Pitzalis, Andrea Maschio, Fabio Busonero, Luca Lai, Robin Skeates, Maria Giuseppina Gradoli, Jessica Beckett, Michele Marongiu, Vittorio Mazzarello, Patrizia Marongiu, Salvatore Rubino, Teresa Rito, Vincent Macaulay, Ornella Semino, Maria Pala, Gonçalo R Abecasis, David Schlessinger, Eduardo Conde-Sousa, Pedro Soares, Martin B Richards, Francesco Cucca, Antonio Torroni
Sardinians are "outliers" in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-specific haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate...
May 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28172616/fastmitocalc-an-ultra-fast-program-to-estimate-mitochondrial-dna-copy-number-from-whole-genome-sequences
#16
Yong Qian, Thomas J Butler, Krista Opsahl-Ong, Nicholas S Giroux, Carlo Sidore, Ramaiah Nagaraja, Francesco Cucca, Luigi Ferrucci, Gonçalo R Abecasis, David Schlessinger, Jun Ding
No abstract text is available yet for this article.
January 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28146470/rare-and-low-frequency-coding-variants-alter-human-adult-height
#17
Eirini Marouli, Mariaelisa Graff, Carolina Medina-Gomez, Ken Sin Lo, Andrew R Wood, Troels R Kjaer, Rebecca S Fine, Yingchang Lu, Claudia Schurmann, Heather M Highland, Sina Rüeger, Gudmar Thorleifsson, Anne E Justice, David Lamparter, Kathleen E Stirrups, Valérie Turcot, Kristin L Young, Thomas W Winkler, Tõnu Esko, Tugce Karaderi, Adam E Locke, Nicholas G D Masca, Maggie C Y Ng, Poorva Mudgal, Manuel A Rivas, Sailaja Vedantam, Anubha Mahajan, Xiuqing Guo, Goncalo Abecasis, Katja K Aben, Linda S Adair, Dewan S Alam, Eva Albrecht, Kristine H Allin, Matthew Allison, Philippe Amouyel, Emil V Appel, Dominique Arveiler, Folkert W Asselbergs, Paul L Auer, Beverley Balkau, Bernhard Banas, Lia E Bang, Marianne Benn, Sven Bergmann, Lawrence F Bielak, Matthias Blüher, Heiner Boeing, Eric Boerwinkle, Carsten A Böger, Lori L Bonnycastle, Jette Bork-Jensen, Michiel L Bots, Erwin P Bottinger, Donald W Bowden, Ivan Brandslund, Gerome Breen, Murray H Brilliant, Linda Broer, Amber A Burt, Adam S Butterworth, David J Carey, Mark J Caulfield, John C Chambers, Daniel I Chasman, Yii-Der Ida Chen, Rajiv Chowdhury, Cramer Christensen, Audrey Y Chu, Massimiliano Cocca, Francis S Collins, James P Cook, Janie Corley, Jordi Corominas Galbany, Amanda J Cox, Gabriel Cuellar-Partida, John Danesh, Gail Davies, Paul I W de Bakker, Gert J de Borst, Simon de Denus, Mark C H de Groot, Renée de Mutsert, Ian J Deary, George Dedoussis, Ellen W Demerath, Anneke I den Hollander, Joe G Dennis, Emanuele Di Angelantonio, Fotios Drenos, Mengmeng Du, Alison M Dunning, Douglas F Easton, Tapani Ebeling, Todd L Edwards, Patrick T Ellinor, Paul Elliott, Evangelos Evangelou, Aliki-Eleni Farmaki, Jessica D Faul, Mary F Feitosa, Shuang Feng, Ele Ferrannini, Marco M Ferrario, Jean Ferrieres, Jose C Florez, Ian Ford, Myriam Fornage, Paul W Franks, Ruth Frikke-Schmidt, Tessel E Galesloot, Wei Gan, Ilaria Gandin, Paolo Gasparini, Vilmantas Giedraitis, Ayush Giri, Giorgia Girotto, Scott D Gordon, Penny Gordon-Larsen, Mathias Gorski, Niels Grarup, Megan L Grove, Vilmundur Gudnason, Stefan Gustafsson, Torben Hansen, Kathleen Mullan Harris, Tamara B Harris, Andrew T Hattersley, Caroline Hayward, Liang He, Iris M Heid, Kauko Heikkilä, Øyvind Helgeland, Jussi Hernesniemi, Alex W Hewitt, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, G Kees Hovingh, Joanna M M Howson, Carel B Hoyng, Paul L Huang, Kristian Hveem, M Arfan Ikram, Erik Ingelsson, Anne U Jackson, Jan-Håkan Jansson, Gail P Jarvik, Gorm B Jensen, Min A Jhun, Yucheng Jia, Xuejuan Jiang, Stefan Johansson, Marit E Jørgensen, Torben Jørgensen, Pekka Jousilahti, J Wouter Jukema, Bratati Kahali, René S Kahn, Mika Kähönen, Pia R Kamstrup, Stavroula Kanoni, Jaakko Kaprio, Maria Karaleftheri, Sharon L R Kardia, Fredrik Karpe, Frank Kee, Renske Keeman, Lambertus A Kiemeney, Hidetoshi Kitajima, Kirsten B Kluivers, Thomas Kocher, Pirjo Komulainen, Jukka Kontto, Jaspal S Kooner, Charles Kooperberg, Peter Kovacs, Jennifer Kriebel, Helena Kuivaniemi, Sébastien Küry, Johanna Kuusisto, Martina La Bianca, Markku Laakso, Timo A Lakka, Ethan M Lange, Leslie A Lange, Carl D Langefeld, Claudia Langenberg, Eric B Larson, I-Te Lee, Terho Lehtimäki, Cora E Lewis, Huaixing Li, Jin Li, Ruifang Li-Gao, Honghuang Lin, Li-An Lin, Xu Lin, Lars Lind, Jaana Lindström, Allan Linneberg, Yeheng Liu, Yongmei Liu, Artitaya Lophatananon, Jian'an Luan, Steven A Lubitz, Leo-Pekka Lyytikäinen, David A Mackey, Pamela A F Madden, Alisa K Manning, Satu Männistö, Gaëlle Marenne, Jonathan Marten, Nicholas G Martin, Angela L Mazul, Karina Meidtner, Andres Metspalu, Paul Mitchell, Karen L Mohlke, Dennis O Mook-Kanamori, Anna Morgan, Andrew D Morris, Andrew P Morris, Martina Müller-Nurasyid, Patricia B Munroe, Mike A Nalls, Matthias Nauck, Christopher P Nelson, Matt Neville, Sune F Nielsen, Kjell Nikus, Pål R Njølstad, Børge G Nordestgaard, Ioanna Ntalla, Jeffrey R O'Connel, Heikki Oksa, Loes M Olde Loohuis, Roel A Ophoff, Katharine R Owen, Chris J Packard, Sandosh Padmanabhan, Colin N A Palmer, Gerard Pasterkamp, Aniruddh P Patel, Alison Pattie, Oluf Pedersen, Peggy L Peissig, Gina M Peloso, Craig E Pennell, Markus Perola, James A Perry, John R B Perry, Thomas N Person, Ailith Pirie, Ozren Polasek, Danielle Posthuma, Olli T Raitakari, Asif Rasheed, Rainer Rauramaa, Dermot F Reilly, Alex P Reiner, Frida Renström, Paul M Ridker, John D Rioux, Neil Robertson, Antonietta Robino, Olov Rolandsson, Igor Rudan, Katherine S Ruth, Danish Saleheen, Veikko Salomaa, Nilesh J Samani, Kevin Sandow, Yadav Sapkota, Naveed Sattar, Marjanka K Schmidt, Pamela J Schreiner, Matthias B Schulze, Robert A Scott, Marcelo P Segura-Lepe, Svati Shah, Xueling Sim, Suthesh Sivapalaratnam, Kerrin S Small, Albert Vernon Smith, Jennifer A Smith, Lorraine Southam, Timothy D Spector, Elizabeth K Speliotes, John M Starr, Valgerdur Steinthorsdottir, Heather M Stringham, Michael Stumvoll, Praveen Surendran, Leen M 't Hart, Katherine E Tansey, Jean-Claude Tardif, Kent D Taylor, Alexander Teumer, Deborah J Thompson, Unnur Thorsteinsdottir, Betina H Thuesen, Anke Tönjes, Gerard Tromp, Stella Trompet, Emmanouil Tsafantakis, Jaakko Tuomilehto, Anne Tybjaerg-Hansen, Jonathan P Tyrer, Rudolf Uher, André G Uitterlinden, Sheila Ulivi, Sander W van der Laan, Andries R Van Der Leij, Cornelia M van Duijn, Natasja M van Schoor, Jessica van Setten, Anette Varbo, Tibor V Varga, Rohit Varma, Digna R Velez Edwards, Sita H Vermeulen, Henrik Vestergaard, Veronique Vitart, Thomas F Vogt, Diego Vozzi, Mark Walker, Feijie Wang, Carol A Wang, Shuai Wang, Yiqin Wang, Nicholas J Wareham, Helen R Warren, Jennifer Wessel, Sara M Willems, James G Wilson, Daniel R Witte, Michael O Woods, Ying Wu, Hanieh Yaghootkar, Jie Yao, Pang Yao, Laura M Yerges-Armstrong, Robin Young, Eleftheria Zeggini, Xiaowei Zhan, Weihua Zhang, Jing Hua Zhao, Wei Zhao, Wei Zhao, He Zheng, Wei Zhou, Jerome I Rotter, Michael Boehnke, Sekar Kathiresan, Mark I McCarthy, Cristen J Willer, Kari Stefansson, Ingrid B Borecki, Dajiang J Liu, Kari E North, Nancy L Heard-Costa, Tune H Pers, Cecilia M Lindgren, Claus Oxvig, Zoltán Kutalik, Fernando Rivadeneira, Ruth J F Loos, Timothy M Frayling, Joel N Hirschhorn, Panos Deloukas, Guillaume Lettre
Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height-increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors...
February 9, 2017: Nature
https://www.readbyqxmd.com/read/28007139/phenotypic-characterization-of-genetically%C3%A2-lowered-human-lipoprotein-a-levels
#18
Connor A Emdin, Amit V Khera, Pradeep Natarajan, Derek Klarin, Hong-Hee Won, Gina M Peloso, Nathan O Stitziel, Akihiro Nomura, Seyedeh M Zekavat, Alexander G Bick, Namrata Gupta, Rosanna Asselta, Stefano Duga, Piera Angelica Merlini, Adolfo Correa, Thorsten Kessler, James G Wilson, Matthew J Bown, Alistair S Hall, Peter S Braund, Nilesh J Samani, Heribert Schunkert, Jaume Marrugat, Roberto Elosua, Ruth McPherson, Martin Farrall, Hugh Watkins, Cristen Willer, Gonçalo R Abecasis, Janine F Felix, Ramachandran S Vasan, Eric Lander, Daniel J Rader, John Danesh, Diego Ardissino, Stacey Gabriel, Danish Saleheen, Sekar Kathiresan
BACKGROUND: Genomic analyses have suggested that the LPA gene and its associated plasma biomarker, lipoprotein(a) (Lp[a]), represent a causal risk factor for coronary heart disease (CHD). As such, lowering Lp(a) levels has emerged as a therapeutic strategy. Beyond target identification, human genetics may contribute to the development of new therapies by defining the full spectrum of beneficial and adverse consequences and by developing a dose-response curve of target perturbation. OBJECTIVES: The goal of this study was to establish the full phenotypic impact of LPA gene variation and to estimate a dose-response curve between genetically altered plasma Lp(a) and risk for CHD...
December 27, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/27984508/characterization-of-adme-gene-variation-in-21-populations-by-exome-sequencing
#19
Daniel H Hovelson, Zhengyu Xue, Matthew Zawistowski, Margaret G Ehm, Elizabeth C Harris, Sophie L Stocker, Annette S Gross, In-Jin Jang, Ichiro Ieiri, Jong-Eun Lee, Lon R Cardon, Stephanie L Chissoe, Gonçalo Abecasis, Matthew R Nelson
OBJECTIVE: Proteins involving absorption, distribution, metabolism, and excretion (ADME) play a critical role in drug pharmacokinetics. The type and frequency of genetic variation in the ADME genes differ among populations. The aim of this study was to systematically investigate common and rare ADME coding variation in diverse ethnic populations by exome sequencing. MATERIALS AND METHODS: Data derived from commercial exome capture arrays and next-generation sequencing were used to characterize coding variation in 298 ADME genes in 251 Northeast Asians and 1181 individuals from the 1000 Genomes Project...
March 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/27876822/a-principal-component-meta-analysis-on-multiple-anthropometric-traits-identifies-novel-loci-for-body-shape
#20
Janina S Ried, Janina Jeff M, Audrey Y Chu, Jennifer L Bragg-Gresham, Jenny van Dongen, Jennifer E Huffman, Tarunveer S Ahluwalia, Gemma Cadby, Niina Eklund, Joel Eriksson, Tõnu Esko, Mary F Feitosa, Anuj Goel, Mathias Gorski, Caroline Hayward, Nancy L Heard-Costa, Anne U Jackson, Eero Jokinen, Stavroula Kanoni, Kati Kristiansson, Zoltán Kutalik, Jari Lahti, Jian'an Luan, Reedik Mägi, Anubha Mahajan, Massimo Mangino, Carolina Medina-Gomez, Keri L Monda, Ilja M Nolte, Louis Pérusse, Inga Prokopenko, Lu Qi, Lynda M Rose, Erika Salvi, Megan T Smith, Harold Snieder, Alena Stančáková, Yun Ju Sung, Ioanna Tachmazidou, Alexander Teumer, Gudmar Thorleifsson, Pim van der Harst, Ryan W Walker, Sophie R Wang, Sarah H Wild, Sara M Willems, Andrew Wong, Weihua Zhang, Eva Albrecht, Alexessander Couto Alves, Stephan J L Bakker, Cristina Barlassina, Traci M Bartz, John Beilby, Claire Bellis, Richard N Bergman, Sven Bergmann, John Blangero, Matthias Blüher, Eric Boerwinkle, Lori L Bonnycastle, Stefan R Bornstein, Marcel Bruinenberg, Harry Campbell, Yii-Der Ida Chen, Charleston W K Chiang, Peter S Chines, Francis S Collins, Fracensco Cucca, L Adrienne Cupples, Francesca D'Avila, Eco J C de Geus, George Dedoussis, Maria Dimitriou, Angela Döring, Johan G Eriksson, Aliki-Eleni Farmaki, Martin Farrall, Teresa Ferreira, Krista Fischer, Nita G Forouhi, Nele Friedrich, Anette Prior Gjesing, Nicola Glorioso, Mariaelisa Graff, Harald Grallert, Niels Grarup, Jürgen Gräßler, Jagvir Grewal, Anders Hamsten, Marie Neergaard Harder, Catharina A Hartman, Maija Hassinen, Nicholas Hastie, Andrew Tym Hattersley, Aki S Havulinna, Markku Heliövaara, Hans Hillege, Albert Hofman, Oddgeir Holmen, Georg Homuth, Jouke-Jan Hottenga, Jennie Hui, Lise Lotte Husemoen, Pirro G Hysi, Aaron Isaacs, Till Ittermann, Shapour Jalilzadeh, Alan L James, Torben Jørgensen, Pekka Jousilahti, Antti Jula, Johanne Marie Justesen, Anne E Justice, Mika Kähönen, Maria Karaleftheri, Kay Tee Khaw, Sirkka M Keinanen-Kiukaanniemi, Leena Kinnunen, Paul B Knekt, Heikki A Koistinen, Ivana Kolcic, Ishminder K Kooner, Seppo Koskinen, Peter Kovacs, Theodosios Kyriakou, Tomi Laitinen, Claudia Langenberg, Alexandra M Lewin, Peter Lichtner, Cecilia M Lindgren, Jaana Lindström, Allan Linneberg, Roberto Lorbeer, Mattias Lorentzon, Robert Luben, Valeriya Lyssenko, Satu Männistö, Paolo Manunta, Irene Mateo Leach, Wendy L McArdle, Barbara Mcknight, Karen L Mohlke, Evelin Mihailov, Lili Milani, Rebecca Mills, May E Montasser, Andrew P Morris, Gabriele Müller, Arthur W Musk, Narisu Narisu, Ken K Ong, Ben A Oostra, Clive Osmond, Aarno Palotie, James S Pankow, Lavinia Paternoster, Brenda W Penninx, Irene Pichler, Maria G Pilia, Ozren Polašek, Peter P Pramstaller, Olli T Raitakari, Tuomo Rankinen, D C Rao, Nigel W Rayner, Rasmus Ribel-Madsen, Treva K Rice, Marcus Richards, Paul M Ridker, Fernando Rivadeneira, Kathy A Ryan, Serena Sanna, Mark A Sarzynski, Salome Scholtens, Robert A Scott, Sylvain Sebert, Lorraine Southam, Thomas Hempel Sparsø, Valgerdur Steinthorsdottir, Kathleen Stirrups, Ronald P Stolk, Konstantin Strauch, Heather M Stringham, Morris A Swertz, Amy J Swift, Anke Tönjes, Emmanouil Tsafantakis, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Liesbeth Vandenput, Erkki Vartiainen, Cristina Venturini, Niek Verweij, Jorma S Viikari, Veronique Vitart, Marie-Claude Vohl, Judith M Vonk, Gérard Waeber, Elisabeth Widén, Gonneke Willemsen, Tom Wilsgaard, Thomas W Winkler, Alan F Wright, Laura M Yerges-Armstrong, Jing Hua Zhao, M Carola Zillikens, Dorret I Boomsma, Claude Bouchard, John C Chambers, Daniel I Chasman, Daniele Cusi, Ron T Gansevoort, Christian Gieger, Torben Hansen, Andrew A Hicks, Frank Hu, Kristian Hveem, Marjo-Riitta Jarvelin, Eero Kajantie, Jaspal S Kooner, Diana Kuh, Johanna Kuusisto, Markku Laakso, Timo A Lakka, Terho Lehtimäki, Andres Metspalu, Inger Njølstad, Claes Ohlsson, Albertine J Oldehinkel, Lyle J Palmer, Oluf Pedersen, Markus Perola, Annette Peters, Bruce M Psaty, Hannu Puolijoki, Rainer Rauramaa, Igor Rudan, Veikko Salomaa, Peter E H Schwarz, Alan R Shudiner, Jan H Smit, Thorkild I A Sørensen, Timothy D Spector, Kari Stefansson, Michael Stumvoll, Angelo Tremblay, Jaakko Tuomilehto, André G Uitterlinden, Matti Uusitupa, Uwe Völker, Peter Vollenweider, Nicholas J Wareham, Hugh Watkins, James F Wilson, Eleftheria Zeggini, Goncalo R Abecasis, Michael Boehnke, Ingrid B Borecki, Panos Deloukas, Cornelia M van Duijn, Caroline Fox, Leif C Groop, Iris M Heid, David J Hunter, Robert C Kaplan, Mark I McCarthy, Kari E North, Jeffrey R O'Connell, David Schlessinger, Unnur Thorsteinsdottir, David P Strachan, Timothy Frayling, Joel N Hirschhorn, Martina Müller-Nurasyid, Ruth J F Loos
Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes...
November 23, 2016: Nature Communications
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