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JOURNAL ARTICLE
Cristopher V Van Hout, Ioanna Tachmazidou, Joshua D Backman, Joshua D Hoffman, Daren Liu, Ashutosh K Pandey, Claudia Gonzaga-Jauregui, Shareef Khalid, Bin Ye, Nilanjana Banerjee, Alexander H Li, Colm O'Dushlaine, Anthony Marcketta, Jeffrey Staples, Claudia Schurmann, Alicia Hawes, Evan Maxwell, Leland Barnard, Alexander Lopez, John Penn, Lukas Habegger, Andrew L Blumenfeld, Xiaodong Bai, Sean O'Keeffe, Ashish Yadav, Kavita Praveen, Marcus Jones, William J Salerno, Wendy K Chung, Ida Surakka, Cristen J Willer, Kristian Hveem, Joseph B Leader, David J Carey, David H Ledbetter, Lon Cardon, George D Yancopoulos, Aris Economides, Giovanni Coppola, Alan R Shuldiner, Suganthi Balasubramanian, Michael Cantor, Matthew R Nelson, John Whittaker, Jeffrey G Reid, Jonathan Marchini, John D Overton, Robert A Scott, Gonçalo R Abecasis, Laura Yerges-Armstrong, Aris Baras
The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1 . Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence...
October 2020: Nature
#22
JOURNAL ARTICLE
Matthew Kerin, Jonathan Marchini
The contribution of gene-by-environment (GxE) interactions for many human traits and diseases is poorly characterized. We propose a Bayesian whole-genome regression model for joint modeling of main genetic effects and GxE interactions in large-scale datasets, such as the UK Biobank, where many environmental variables have been measured. The method is called LEMMA (Linear Environment Mixed Model Analysis) and estimates a linear combination of environmental variables, called an environmental score (ES), that interacts with genetic markers throughout the genome...
August 27, 2020: American Journal of Human Genetics
#23
JOURNAL ARTICLE
Nicola J Armstrong, Karen A Mather, Muralidharan Sargurupremraj, Maria J Knol, Rainer Malik, Claudia L Satizabal, Lisa R Yanek, Wei Wen, Vilmundur G Gudnason, Nicole D Dueker, Lloyd T Elliott, Edith Hofer, Joshua Bis, Neda Jahanshad, Shuo Li, Mark A Logue, Michelle Luciano, Markus Scholz, Albert V Smith, Stella Trompet, Dina Vojinovic, Rui Xia, Fidel Alfaro-Almagro, David Ames, Najaf Amin, Philippe Amouyel, Alexa S Beiser, Henry Brodaty, Ian J Deary, Christine Fennema-Notestine, Piyush G Gampawar, Rebecca Gottesman, Ludovica Griffanti, Clifford R Jack, Mark Jenkinson, Jiyang Jiang, Brian G Kral, John B Kwok, Leonie Lampe, David C M Liewald, Pauline Maillard, Jonathan Marchini, Mark E Bastin, Bernard Mazoyer, Lukas Pirpamer, José Rafael Romero, Gennady V Roshchupkin, Peter R Schofield, Matthias L Schroeter, David J Stott, Anbupalam Thalamuthu, Julian Trollor, Christophe Tzourio, Jeroen van der Grond, Meike W Vernooij, Veronica A Witte, Margaret J Wright, Qiong Yang, Zoe Morris, Siggi Siggurdsson, Bruce Psaty, Arno Villringer, Helena Schmidt, Asta K Haberg, Cornelia M van Duijn, J Wouter Jukema, Martin Dichgans, Ralph L Sacco, Clinton B Wright, William S Kremen, Lewis C Becker, Paul M Thompson, Thomas H Mosley, Joanna M Wardlaw, M Arfan Ikram, Hieab H H Adams, Sudha Seshadri, Perminder S Sachdev, Stephen M Smith, Lenore Launer, William Longstreth, Charles DeCarli, Reinhold Schmidt, Myriam Fornage, Stephanie Debette, Paul A Nyquist
BACKGROUND AND PURPOSE: Periventricular white matter hyperintensities (WMH; PVWMH) and deep WMH (DWMH) are regional classifications of WMH and reflect proposed differences in cause. In the first study, to date, we undertook genome-wide association analyses of DWMH and PVWMH to show that these phenotypes have different genetic underpinnings. METHODS: Participants were aged 45 years and older, free of stroke and dementia. We conducted genome-wide association analyses of PVWMH and DWMH in 26,654 participants from CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology), ENIGMA (Enhancing Neuro-Imaging Genetics Through Meta-Analysis), and the UKB (UK Biobank)...
July 2020: Stroke; a Journal of Cerebral Circulation
#24
JOURNAL ARTICLE
Na Cai, Tim B Bigdeli, Warren W Kretzschmar, Yihan Li, Jieqin Liang, Jingchu Hu, Roseann E Peterson, Silviu Bacanu, Bradley Todd Webb, Brien Riley, Qibin Li, Jonathan Marchini, Richard Mott, Kenneth S Kendler, Jonathan Flint
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
April 16, 2020: Scientific Data
#25
JOURNAL ARTICLE
Olivier Delaneau, Jean-François Zagury, Matthew R Robinson, Jonathan L Marchini, Emmanouil T Dermitzakis
The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads...
November 28, 2019: Nature Communications
#26
JOURNAL ARTICLE
Akira Wiberg, Michael Ng, Yasser Al Omran, Fidel Alfaro-Almagro, Paul McCarthy, Jonathan Marchini, David L Bennett, Stephen Smith, Gwenaëlle Douaud, Dominic Furniss
Ninety per cent of the human population has been right-handed since the Paleolithic, yet the brain signature and genetic basis of handedness remain poorly characterized. Here, we correlated brain imaging phenotypes from ∼9000 UK Biobank participants with handedness, and with loci found significantly associated with handedness after we performed genome-wide association studies (GWAS) in ∼400 000 of these participants. Our imaging-handedness analysis revealed an increase in functional connectivity between left and right language networks in left-handers...
October 1, 2019: Brain
#27
JOURNAL ARTICLE
Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon R Myers, Donald F Conrad
To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyse a novel 57,600-cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3 , Hormad1 , Cul4a or Cnp . By jointly analysing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programmes, mutant-specific pathological processes, and technical effects, and provide a framework for imputation...
June 25, 2019: ELife
#28
JOURNAL ARTICLE
Jeroen Mollink, Stephen M Smith, Lloyd T Elliott, Michiel Kleinnijenhuis, Marlies Hiemstra, Fidel Alfaro-Almagro, Jonathan Marchini, Anne-Marie van Cappellen van Walsum, Saad Jbabdi, Karla L Miller
Microscopic features (that is, microstructure) of axons affect neural circuit activity through characteristics such as conduction speed. To what extent axonal microstructure in white matter relates to functional connectivity (synchrony) between brain regions is largely unknown. Using MRI data in 11,354 subjects, we constructed multivariate models that predict functional connectivity of pairs of brain regions from the microstructural signature of white matter pathways that connect them. Microstructure-derived models provided predictions of functional connectivity that explained 3...
May 2019: Nature Neuroscience
#29
EDITORIAL
Giorgio Sirugo, Scott M Williams, Sarah A Tishkoff, Heather J Cordell, Jonathan Marchini, Gregory S Barsh, Gregory P Copenhaver
No abstract text is available yet for this article.
March 2019: PLoS Genetics
#30
JOURNAL ARTICLE
Clare Bycroft, Colin Freeman, Desislava Petkova, Gavin Band, Lloyd T Elliott, Kevin Sharp, Allan Motyer, Damjan Vukcevic, Olivier Delaneau, Jared O'Connell, Adrian Cortes, Samantha Welsh, Alan Young, Mark Effingham, Gil McVean, Stephen Leslie, Naomi Allen, Peter Donnelly, Jonathan Marchini
The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at recruitment. The open resource is unique in its size and scope. A rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. Follow-up information is provided by linking health and medical records...
October 2018: Nature
#31
JOURNAL ARTICLE
Lloyd T Elliott, Kevin Sharp, Fidel Alfaro-Almagro, Sinan Shi, Karla L Miller, Gwenaëlle Douaud, Jonathan Marchini, Stephen M Smith
The genetic architecture of brain structure and function is largely unknown. To investigate this, we carried out genome-wide association studies of 3,144 functional and structural brain imaging phenotypes from UK Biobank (discovery dataset 8,428 subjects). Here we show that many of these phenotypes are heritable. We identify 148 clusters of associations between single nucleotide polymorphisms and imaging phenotypes that replicate at P < 0.05, when we would expect 21 to replicate by chance. Notable significant, interpretable associations include: iron transport and storage genes, related to magnetic susceptibility of subcortical brain tissue; extracellular matrix and epidermal growth factor genes, associated with white matter micro-structure and lesions; genes that regulate mid-line axon development, associated with organization of the pontine crossing tract; and overall 17 genes involved in development, pathway signalling and plasticity...
October 2018: Nature
#32
JOURNAL ARTICLE
Anubha Mahajan, Daniel Taliun, Matthias Thurner, Neil R Robertson, Jason M Torres, N William Rayner, Anthony J Payne, Valgerdur Steinthorsdottir, Robert A Scott, Niels Grarup, James P Cook, Ellen M Schmidt, Matthias Wuttke, Chloé Sarnowski, Reedik Mägi, Jana Nano, Christian Gieger, Stella Trompet, Cécile Lecoeur, Michael H Preuss, Bram Peter Prins, Xiuqing Guo, Lawrence F Bielak, Jennifer E Below, Donald W Bowden, John Campbell Chambers, Young Jin Kim, Maggie C Y Ng, Lauren E Petty, Xueling Sim, Weihua Zhang, Amanda J Bennett, Jette Bork-Jensen, Chad M Brummett, Mickaël Canouil, Kai-Uwe Ec Kardt, Krista Fischer, Sharon L R Kardia, Florian Kronenberg, Kristi Läll, Ching-Ti Liu, Adam E Locke, Jian'an Luan, Ioanna Ntalla, Vibe Nylander, Sebastian Schönherr, Claudia Schurmann, Loïc Yengo, Erwin P Bottinger, Ivan Brandslund, Cramer Christensen, George Dedoussis, Jose C Florez, Ian Ford, Oscar H Franco, Timothy M Frayling, Vilmantas Giedraitis, Sophie Hackinger, Andrew T Hattersley, Christian Herder, M Arfan Ikram, Martin Ingelsson, Marit E Jørgensen, Torben Jørgensen, Jennifer Kriebel, Johanna Kuusisto, Symen Ligthart, Cecilia M Lindgren, Allan Linneberg, Valeriya Lyssenko, Vasiliki Mamakou, Thomas Meitinger, Karen L Mohlke, Andrew D Morris, Girish Nadkarni, James S Pankow, Annette Peters, Naveed Sattar, Alena Stančáková, Konstantin Strauch, Kent D Taylor, Barbara Thorand, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Jaakko Tuomilehto, Daniel R Witte, Josée Dupuis, Patricia A Peyser, Eleftheria Zeggini, Ruth J F Loos, Philippe Froguel, Erik Ingelsson, Lars Lind, Leif Groop, Markku Laakso, Francis S Collins, J Wouter Jukema, Colin N A Palmer, Harald Grallert, Andres Metspalu, Abbas Dehghan, Anna Köttgen, Goncalo R Abecasis, James B Meigs, Jerome I Rotter, Jonathan Marchini, Oluf Pedersen, Torben Hansen, Claudia Langenberg, Nicholas J Wareham, Kari Stefansson, Anna L Gloyn, Andrew P Morris, Michael Boehnke, Mark I McCarthy
We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency <5%, 14 with estimated allelic odds ratio >2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence)...
November 2018: Nature Genetics
#33
JOURNAL ARTICLE
Diane R Wang, Francisco J Agosto-Pérez, Dmytro Chebotarov, Yuxin Shi, Jonathan Marchini, Melissa Fitzgerald, Kenneth L McNally, Nickolai Alexandrov, Susan R McCouch
As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of integrating resources for downstream applications. While a number of imputation software packages are available, the limitations to utilization for the rice community include high computational demand and lack of a reference panel...
August 29, 2018: Nature Communications
#34
JOURNAL ARTICLE
Naomi R Wray, Stephan Ripke, Manuel Mattheisen, Maciej Trzaskowski, Enda M Byrne, Abdel Abdellaoui, Mark J Adams, Esben Agerbo, Tracy M Air, Till M F Andlauer, Silviu-Alin Bacanu, Marie Bækvad-Hansen, Aartjan F T Beekman, Tim B Bigdeli, Elisabeth B Binder, Douglas R H Blackwood, Julien Bryois, Henriette N Buttenschøn, Jonas Bybjerg-Grauholm, Na Cai, Enrique Castelao, Jane Hvarregaard Christensen, Toni-Kim Clarke, Jonathan I R Coleman, Lucía Colodro-Conde, Baptiste Couvy-Duchesne, Nick Craddock, Gregory E Crawford, Cheynna A Crowley, Hassan S Dashti, Gail Davies, Ian J Deary, Franziska Degenhardt, Eske M Derks, Nese Direk, Conor V Dolan, Erin C Dunn, Thalia C Eley, Nicholas Eriksson, Valentina Escott-Price, Farnush Hassan Farhadi Kiadeh, Hilary K Finucane, Andreas J Forstner, Josef Frank, Héléna A Gaspar, Michael Gill, Paola Giusti-Rodríguez, Fernando S Goes, Scott D Gordon, Jakob Grove, Lynsey S Hall, Eilis Hannon, Christine Søholm Hansen, Thomas F Hansen, Stefan Herms, Ian B Hickie, Per Hoffmann, Georg Homuth, Carsten Horn, Jouke-Jan Hottenga, David M Hougaard, Ming Hu, Craig L Hyde, Marcus Ising, Rick Jansen, Fulai Jin, Eric Jorgenson, James A Knowles, Isaac S Kohane, Julia Kraft, Warren W Kretzschmar, Jesper Krogh, Zoltán Kutalik, Jacqueline M Lane, Yihan Li, Yun Li, Penelope A Lind, Xiaoxiao Liu, Leina Lu, Donald J MacIntyre, Dean F MacKinnon, Robert M Maier, Wolfgang Maier, Jonathan Marchini, Hamdi Mbarek, Patrick McGrath, Peter McGuffin, Sarah E Medland, Divya Mehta, Christel M Middeldorp, Evelin Mihailov, Yuri Milaneschi, Lili Milani, Jonathan Mill, Francis M Mondimore, Grant W Montgomery, Sara Mostafavi, Niamh Mullins, Matthias Nauck, Bernard Ng, Michel G Nivard, Dale R Nyholt, Paul F O'Reilly, Hogni Oskarsson, Michael J Owen, Jodie N Painter, Carsten Bøcker Pedersen, Marianne Giørtz Pedersen, Roseann E Peterson, Erik Pettersson, Wouter J Peyrot, Giorgio Pistis, Danielle Posthuma, Shaun M Purcell, Jorge A Quiroz, Per Qvist, John P Rice, Brien P Riley, Margarita Rivera, Saira Saeed Mirza, Richa Saxena, Robert Schoevers, Eva C Schulte, Ling Shen, Jianxin Shi, Stanley I Shyn, Engilbert Sigurdsson, Grant B C Sinnamon, Johannes H Smit, Daniel J Smith, Hreinn Stefansson, Stacy Steinberg, Craig A Stockmeier, Fabian Streit, Jana Strohmaier, Katherine E Tansey, Henning Teismann, Alexander Teumer, Wesley Thompson, Pippa A Thomson, Thorgeir E Thorgeirsson, Chao Tian, Matthew Traylor, Jens Treutlein, Vassily Trubetskoy, André G Uitterlinden, Daniel Umbricht, Sandra Van der Auwera, Albert M van Hemert, Alexander Viktorin, Peter M Visscher, Yunpeng Wang, Bradley T Webb, Shantel Marie Weinsheimer, Jürgen Wellmann, Gonneke Willemsen, Stephanie H Witt, Yang Wu, Hualin S Xi, Jian Yang, Futao Zhang, Volker Arolt, Bernhard T Baune, Klaus Berger, Dorret I Boomsma, Sven Cichon, Udo Dannlowski, E C J de Geus, J Raymond DePaulo, Enrico Domenici, Katharina Domschke, Tõnu Esko, Hans J Grabe, Steven P Hamilton, Caroline Hayward, Andrew C Heath, David A Hinds, Kenneth S Kendler, Stefan Kloiber, Glyn Lewis, Qingqin S Li, Susanne Lucae, Pamela F A Madden, Patrik K Magnusson, Nicholas G Martin, Andrew M McIntosh, Andres Metspalu, Ole Mors, Preben Bo Mortensen, Bertram Müller-Myhsok, Merete Nordentoft, Markus M Nöthen, Michael C O'Donovan, Sara A Paciga, Nancy L Pedersen, Brenda W J H Penninx, Roy H Perlis, David J Porteous, James B Potash, Martin Preisig, Marcella Rietschel, Catherine Schaefer, Thomas G Schulze, Jordan W Smoller, Kari Stefansson, Henning Tiemeier, Rudolf Uher, Henry Völzke, Myrna M Weissman, Thomas Werge, Ashley R Winslow, Cathryn M Lewis, Douglas F Levinson, Gerome Breen, Anders D Børglum, Patrick F Sullivan
Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association meta-analysis based in 135,458 cases and 344,901 controls and identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal...
May 2018: Nature Genetics
#35
JOURNAL ARTICLE
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
#36
JOURNAL ARTICLE
Na Cai, Tim B Bigdeli, Warren W Kretzschmar, Yihan Li, Jieqin Liang, Jingchu Hu, Roseann E Peterson, Silviu Bacanu, Bradley Todd Webb, Brien Riley, Qibin Li, Jonathan Marchini, Richard Mott, Kenneth S Kendler, Jonathan Flint
The China, Oxford and Virginia Commonwealth University Experimental Research on Genetic Epidemiology (CONVERGE) project on Major Depressive Disorder (MDD) sequenced 11,670 female Han Chinese at low-coverage (1.7X), providing the first large-scale whole genome sequencing resource representative of the largest ethnic group in the world. Samples are collected from 58 hospitals from 23 provinces around China. We are able to call 22 million high quality single nucleotide polymorphisms (SNP) from the nuclear genome, representing the largest SNP call set from an East Asian population to date...
February 14, 2017: Scientific Data
#37
JOURNAL ARTICLE
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima, John J Lambourne, Suthesh Sivapalaratnam, Kate Downes, Kousik Kundu, Lorenzo Bomba, Kim Berentsen, John R Bradley, Louise C Daugherty, Olivier Delaneau, Kathleen Freson, Stephen F Garner, Luigi Grassi, Jose Guerrero, Matthias Haimel, Eva M Janssen-Megens, Anita Kaan, Mihir Kamat, Bowon Kim, Amit Mandoli, Jonathan Marchini, Joost H A Martens, Stuart Meacham, Karyn Megy, Jared O'Connell, Romina Petersen, Nilofar Sharifi, Simon M Sheard, James R Staley, Salih Tuna, Martijn van der Ent, Klaudia Walter, Shuang-Yin Wang, Eleanor Wheeler, Steven P Wilder, Valentina Iotchkova, Carmel Moore, Jennifer Sambrook, Hendrik G Stunnenberg, Emanuele Di Angelantonio, Stephen Kaptoge, Taco W Kuijpers, Enrique Carrillo-de-Santa-Pau, David Juan, Daniel Rico, Alfonso Valencia, Lu Chen, Bing Ge, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yang, Roderic Guigo, Stephan Beck, Dirk S Paul, Tomi Pastinen, David Bujold, Guillaume Bourque, Mattia Frontini, John Danesh, David J Roberts, Willem H Ouwehand, Adam S Butterworth, Nicole Soranzo
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains...
November 17, 2016: Cell
#38
REVIEW
Christopher I Amos, Joe Dennis, Zhaoming Wang, Jinyoung Byun, Fredrick R Schumacher, Simon A Gayther, Graham Casey, David J Hunter, Thomas A Sellers, Stephen B Gruber, Alison M Dunning, Kyriaki Michailidou, Laura Fachal, Kimberly Doheny, Amanda B Spurdle, Yafang Li, Xiangjun Xiao, Jane Romm, Elizabeth Pugh, Gerhard A Coetzee, Dennis J Hazelett, Stig E Bojesen, Charlisse Caga-Anan, Christopher A Haiman, Ahsan Kamal, Craig Luccarini, Daniel Tessier, Daniel Vincent, François Bacot, David J Van Den Berg, Stefanie Nelson, Stephen Demetriades, David E Goldgar, Fergus J Couch, Judith L Forman, Graham G Giles, David V Conti, Heike Bickeböller, Angela Risch, Melanie Waldenberger, Irene Brüske-Hohlfeld, Belynda D Hicks, Hua Ling, Lesley McGuffog, Andrew Lee, Karoline Kuchenbaecker, Penny Soucy, Judith Manz, Julie M Cunningham, Katja Butterbach, Zsofia Kote-Jarai, Peter Kraft, Liesel FitzGerald, Sara Lindström, Marcia Adams, James D McKay, Catherine M Phelan, Sara Benlloch, Linda E Kelemen, Paul Brennan, Marjorie Riggan, Tracy A O'Mara, Hongbing Shen, Yongyong Shi, Deborah J Thompson, Marc T Goodman, Sune F Nielsen, Andrew Berchuck, Sylvie Laboissiere, Stephanie L Schmit, Tameka Shelford, Christopher K Edlund, Jack A Taylor, John K Field, Sue K Park, Kenneth Offit, Mads Thomassen, Rita Schmutzler, Laura Ottini, Rayjean J Hung, Jonathan Marchini, Ali Amin Al Olama, Ulrike Peters, Rosalind A Eeles, Michael F Seldin, Elizabeth Gillanders, Daniela Seminara, Antonis C Antoniou, Paul D P Pharoah, Georgia Chenevix-Trench, Stephen J Chanock, Jacques Simard, Douglas F Easton
BACKGROUND: Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits...
January 2017: Cancer Epidemiology, Biomarkers & Prevention
#39
MULTICENTER STUDY
Sander W van der Laan, Tove Fall, Aicha Soumaré, Alexander Teumer, Sanaz Sedaghat, Jens Baumert, Delilah Zabaneh, Jessica van Setten, Ivana Isgum, Tessel E Galesloot, Johannes Arpegård, Philippe Amouyel, Stella Trompet, Melanie Waldenberger, Marcus Dörr, Patrik K Magnusson, Vilmantas Giedraitis, Anders Larsson, Andrew P Morris, Janine F Felix, Alanna C Morrison, Nora Franceschini, Joshua C Bis, Maryam Kavousi, Christopher O'Donnell, Fotios Drenos, Vinicius Tragante, Patricia B Munroe, Rainer Malik, Martin Dichgans, Bradford B Worrall, Jeanette Erdmann, Christopher P Nelson, Nilesh J Samani, Heribert Schunkert, Jonathan Marchini, Riyaz S Patel, Aroon D Hingorani, Lars Lind, Nancy L Pedersen, Jacqueline de Graaf, Lambertus A L M Kiemeney, Sebastian E Baumeister, Oscar H Franco, Albert Hofman, André G Uitterlinden, Wolfgang Koenig, Christa Meisinger, Annette Peters, Barbara Thorand, J Wouter Jukema, Bjørn Odvar Eriksen, Ingrid Toft, Tom Wilsgaard, N Charlotte Onland-Moret, Yvonne T van der Schouw, Stéphanie Debette, Meena Kumari, Per Svensson, Pim van der Harst, Mika Kivimaki, Brendan J Keating, Naveed Sattar, Abbas Dehghan, Alex P Reiner, Erik Ingelsson, Hester M den Ruijter, Paul I W de Bakker, Gerard Pasterkamp, Johan Ärnlöv, Michael V Holmes, Folkert W Asselbergs
BACKGROUND: Epidemiological studies show that high circulating cystatin C is associated with risk of cardiovascular disease (CVD), independent of creatinine-based renal function measurements. It is unclear whether this relationship is causal, arises from residual confounding, and/or is a consequence of reverse causation. OBJECTIVES: The aim of this study was to use Mendelian randomization to investigate whether cystatin C is causally related to CVD in the general population...
August 30, 2016: Journal of the American College of Cardiology
#40
JOURNAL ARTICLE
Victoria Hore, Ana Viñuela, Alfonso Buil, Julian Knight, Mark I McCarthy, Kerrin Small, Jonathan Marchini
Genome-wide association studies of gene expression traits and other cellular phenotypes have successfully identified links between genetic variation and biological processes. The majority of discoveries have uncovered cis-expression quantitative trait locus (eQTL) effects via mass univariate testing of SNPs against gene expression in single tissues. Here we present a Bayesian method for multiple-tissue experiments focusing on uncovering gene networks linked to genetic variation. Our method decomposes the 3D array (or tensor) of gene expression measurements into a set of latent components...
September 2016: Nature Genetics
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