Smoking-by-genotype interaction in type 2 diabetes risk and fasting glucose
Peitao Wu,Denis Rybin,Lawrence F. Bielak,Mary F. Feitosa,Nora Franceschini,Yize Li,Yingchang Lu,Jonathan Marten,Solomon K. Musani,Raymond Noordam,Sridharan Raghavan,Sridharan Raghavan,Sridharan Raghavan,Lynda M. Rose,Karen Schwander,Albert V. Smith,Salman M. Tajuddin,Dina Vojinovic,Najaf Amin,Donna K. Arnett,Erwin P. Bottinger,Ayse Demirkan,Jose C. Florez,Jose C. Florez,Mohsen Ghanbari,Mohsen Ghanbari,Tamara B. Harris,Lenore J. Launer,Jingmin Liu,Jun Liu,Dennis O. Mook-Kanamori,Alison D. Murray,Mike A. Nalls,Patricia A. Peyser,André G. Uitterlinden,Trudy Voortman,Claude Bouchard,Daniel I. Chasman,Daniel I. Chasman,Adolfo Correa,Renée de Mutsert,Michele K. Evans,Vilmundur Gudnason,Caroline Hayward,Linda Kao,Sharon L.R. Kardia,Charles Kooperberg,Ruth J. F. Loos,Michael M. Province,Tuomo Rankinen,Susan Redline,Susan Redline,Susan Redline,Paul M. Ridker,Paul M. Ridker,Jerome I. Rotter,David S. Siscovick,Blair H. Smith,Cornelia M. van Duijn,Alan B. Zonderman,D. C. Rao,James G. Wilson,Josée Dupuis,Josée Dupuis,James B. Meigs,James B. Meigs,Ching-Ti Liu,Jason L. Vassy,Jason L. Vassy +68 more
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TLDR
The identification of loci exhibiting potential interaction with baseline smoking status provides evidence for genetic interactions with smoking exposure that may explain some of the heterogeneity in the association between smoking and T2D.Abstract:
Smoking is a potentially causal behavioral risk factor for type 2 diabetes (T2D), but not all smokers develop T2D. It is unknown whether genetic factors partially explain this variation. We performed genome-environment-wide interaction studies to identify loci exhibiting potential interaction with baseline smoking status (ever vs. never) on incident T2D and fasting glucose (FG). Analyses were performed in participants of European (EA) and African ancestry (AA) separately. Discovery analyses were conducted using genotype data from the 50,000-single-nucleotide polymorphism (SNP) ITMAT-Broad-CARe (IBC) array in 5 cohorts from from the Candidate Gene Association Resource Consortium (n = 23,189). Replication was performed in up to 16 studies from the Cohorts for Heart Aging Research in Genomic Epidemiology Consortium (n = 74,584). In meta-analysis of discovery and replication estimates, 5 SNPs met at least one criterion for potential interaction with smoking on incident T2D at p<1x10-7 (adjusted for multiple hypothesis-testing with the IBC array). Two SNPs had significant joint effects in the overall model and significant main effects only in one smoking stratum: rs140637 (FBN1) in AA individuals had a significant main effect only among smokers, and rs1444261 (closest gene C2orf63) in EA individuals had a significant main effect only among nonsmokers. Three additional SNPs were identified as having potential interaction by exhibiting a significant main effects only in smokers: rs1801232 (CUBN) in AA individuals, rs12243326 (TCF7L2) in EA individuals, and rs4132670 (TCF7L2) in EA individuals. No SNP met significance for potential interaction with smoking on baseline FG. The identification of these loci provides evidence for genetic interactions with smoking exposure that may explain some of the heterogeneity in the association between smoking and T2D.read more
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The genetic architecture of type 2 diabetes
Christian Fuchsberger,Jason Flannick,Tanya M. Teslovich,Anubha Mahajan,Vineeta Agarwala,Kyle J. Gaulton,Clement Ma,Pierre Fontanillas,Loukas Moutsianas,Davis J. McCarthy,Manuel A. Rivas,John R. B. Perry,Xueling Sim,Thomas W. Blackwell,Neil Robertson,N. William Rayner,Pablo Cingolani,Adam E. Locke,Juan Fernandez Tajes,Heather M. Highland,Josée Dupuis,Peter S. Chines,Cecilia M. Lindgren,Christopher Hartl,Anne U. Jackson,Han Chen,Jeroen R. Huyghe,Martijn van de Bunt,Richard D. Pearson,Ashok Kumar,Martina Mueller-Nurasyid,Niels Grarup,Heather M. Stringham,Eric R. Gamazon,Jae-Hoon Lee,Yi Chen,Robert A. Scott,Jennifer E. Below,Peng Chen,Jinyan Huang,Min Jin Go,Michael L. Stitzel,Dorota Pasko,Stephen C. J. Parker,Tibor V. Varga,Todd Green,Nicola L. Beer,Aaron G. Day-Williams,Teresa Ferreira,Tasha E. Fingerlin,Momoko Horikoshi,Cheng Hu,Iksoo Huh,Mohammad Kamran Ikram,Bong-Jo Kim,Yongkang Kim,Young-Jin Kim,Min-Seok Kwon,Juyoung Lee,Selyeong Lee,Keng-Han Lin,Taylor J. Maxwell,Yoshihiko Nagai,Xu Wang,Ryan P. Welch,Joon Yoon,Weihua Zhang,Nir Barzilai,Benjamin F. Voight,Bok-Ghee Han,Christopher P. Jenkinson,Teemu Kuulasmaa,Johanna Kuusisto,Alisa K. Manning,Maggie C.Y. Ng,Nicholette D. Palmer,Beverley Balkau,Alena Stančáková,Hanna E. Abboud,Heiner Boeing,Vilmantas Giedraitis,Dorairaj Prabhakaran,Omri Gottesman,James Scott,Jason Carey,Phoenix Kwan,George B. Grant,Joshua D. Smith,Benjamin M. Neale,Shaun Purcell,Adam S. Butterworth,Joanna M. M. Howson,Heung Man Lee,Yingchang Lu,Soo Heon Kwak,Wei Zhao,John Danesh,Vincent K. L. Lam,Kyong Soo Park,Danish Saleheen,Wing-Yee So,Claudia H. T. Tam,Uzma Afzal,David Aguilar,Rector Arya,Tin Aung,Edmund Chan,Carmen Navarro,Ching-Yu Cheng,Domenico Palli,Adolfo Correa,Joanne E. Curran,Denis Rybin,Vidya S. Farook,Sharon P. Fowler,Barry I. Freedman,Michael Griswold,Daniel E. Hale,Pamela J. Hicks,Chiea Chuen Khor,Satish Kumar,Benjamin Lehne,Dorothée Thuillier,Wei-Yen Lim,Jianjun Liu,Yvonne T. van der Schouw,Marie Loh,Solomon K. Musani,Sobha Puppala,William R. Scott,Loic Yengo,Sian-Tsung Tan,Herman A. Taylor,Farook Thameem,Gregory P. Wilson,Tien Yin Wong,Pål R. Njølstad,Jonathan C. Levy,Massimo Mangino,Lori L. Bonnycastle,Thomas Schwarzmayr,João Fadista,Gabriela L. Surdulescu,Christian Herder,Christopher J. Groves,Thomas Wieland,Jette Bork-Jensen,Ivan Brandslund,Cramer Christensen,Heikki A. Koistinen,Alex S. F. Doney,Leena Kinnunen,Tõnu Esko,Andrew Farmer,Liisa Hakaste,Dylan Hodgkiss,Jasmina Kravic,Valeriya Lyssenko,Mette Hollensted,Marit E. Jørgensen,Torben Jørgensen,Claes Ladenvall,Johanne Marie Justesen,Annemari Käräjämäki,Jennifer Kriebel,Wolfgang Rathmann,Lars Lannfelt,Torsten Lauritzen,Narisu Narisu,Allan Linneberg,Olle Melander,Lili Milani,Matt Neville,Marju Orho-Melander,Lu Qi,Qibin Qi,Michael Roden,Olov Rolandsson,Amy J. Swift,Anders Rosengren,Kathleen Stirrups,Andrew R. Wood,Evelin Mihailov,Christine Blancher,Mauricio O. Carneiro,Jared Maguire,Ryan Poplin,Khalid Shakir,Timothy R. Fennell,Mark A. DePristo,Martin Hrabé de Angelis,Panos Deloukas,Anette P. Gjesing,Goo Jun,Peter M. Nilsson,Jacquelyn Murphy,Robert C. Onofrio,Barbara Thorand,Torben Hansen,Christa Meisinger,Frank B. Hu,Bo Isomaa,Fredrik Karpe,Liming Liang,Annette Peters,Cornelia Huth,Stephen O'Rahilly,Colin N. A. Palmer,Oluf Pedersen,Rainer Rauramaa,Jaakko Tuomilehto,Veikko Salomaa,Richard M. Watanabe,Ann-Christine Syvänen,Richard N. Bergman,Dwaipayan Bharadwaj,Erwin P. Bottinger,Yoon Shin Cho,Giriraj R. Chandak,Juliana C.N. Chan,Kee Seng Chia,Mark J. Daly,Shah Ebrahim,Claudia Langenberg,Paul Elliott,Kathleen A. Jablonski,Donna M. Lehman,Weiping Jia,Ronald C.W. Ma,Toni I. Pollin,Manjinder S. Sandhu,Nikhil Tandon,Philippe Froguel,Inês Barroso,Yik Ying Teo,Eleftheria Zeggini,Ruth J. F. Loos,Kerrin S. Small,Janina S. Ried,Ralph A. DeFronzo,Harald Grallert,Benjamin Glaser,Andres Metspalu,Nicholas J. Wareham,Mark Walker,Eric Banks,Christian Gieger,Erik Ingelsson,Hae Kyung Im,Thomas Illig,Paul W. Franks,Gemma Buck,Joseph Trakalo,David Buck,Inga Prokopenko,Reedik Mägi,Lars Lind,Yossi Farjoun,Katharine R. Owen,Anna L. Gloyn,Konstantin Strauch,Tiinamaija Tuomi,Jaspal S. Kooner,Jong-Young Lee,Taesung Park,Peter Donnelly,Andrew D. Morris,Andrew T. Hattersley,Donald W. Bowden,Francis S. Collins,Gil Atzmon,John C. Chambers,Tim D. Spector,Markku Laakso,Tim M. Strom,Graeme I. Bell,John Blangero,Ravindranath Duggirala,E. Shyong Tai,Gilean McVean,Craig L. Hanis,James G. Wilson,Mark Seielstad,Timothy M. Frayling,James B. Meigs,Nancy J. Cox,Robert Sladek,Eric S. Lander,Stacey Gabriel,Noël P. Burtt,Karen L. Mohlke,Thomas Meitinger,Leif Groop,Gonçalo R. Abecasis,Jose C. Florez,Laura J. Scott,Andrew P. Morris,Hyun Min Kang,Michael Boehnke,David Altshuler,Mark I. McCarthy +300 more
TL;DR: Large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes, but most fell within regions previously identified by genome-wide association studies.
Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps
Anubha Mahajan,Daniel Taliun,Matthias Thurner,Neil R. Robertson,Jason M. Torres,N. William Rayner,Anthony Payne,Valgerdur Steinthorsdottir,Robert A. Scott,Niels Grarup,James P. Cook,Ellen M. Schmidt,Matthias Wuttke,Chloé Sarnowski,Reedik Magill,Jana Nano,Christian Gieger,Stella Trompet,Cécile Lecoeur,Michael Preuss,Bram P. Prins,Xiuqing Guo,Lawrence F. Bielak,Jennifer E. Below,Donald W. Bowden,John C. 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,Loanna Ntalla,Vibe Nylander,Sebastian Schoenherr,Claudia Schurmann,Loic Yengo,Erwin P. Bottinger,Ivan Brandslund,Cramer Christensen,George Dedoussis,Jose C. Florez,Ian Ford,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 N. 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 Koettgen,Gonçalo R. Abecasis,James B. Meigs,Rotter, Jerome, I,Jonathan Marchini,Oluf Pedersen,Torben Hansen,Claudia Langenberg,Nicholas J. Wareham,Kari Stefansson,Anna L. Gloyn,Andrew P. Morris,Michael Boehnke,McCarthy, Mark, I +113 more
Abstract: 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).Combining 32 genome-wide association studies with high-density imputation provides a comprehensive view of the genetic contribution to type 2 diabetes in individuals of European ancestry with respect to locus discovery, causal-variant resolution, and mechanistic insight.
Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci
A. Mesut Erzurumluoglu,Mengzhen Liu,Victoria E. Jackson,Daniel R. Barnes,Gargi Datta,Carl A. Melbourne,Robin Young,Chiara Batini,Praveen Surendran,Tao Jiang,Sheikh Daud Adnan,Saima Afaq,Arpana Agrawal,Elisabeth Altmaier,Antonis C. Antoniou,Folkert W. Asselbergs,Clemens Baumbach,Laura J. Bierut,Sarah Bertelsen,Michael Boehnke,Michiel L. Bots,David M. Brazel,John C. Chambers,Jenny Chang-Claude,Chu Chen,Janie Corley,Yi-Ling Chou,Sean P. David,Rudolf A. de Boer,Christiaan de Leeuw,Joe Dennis,Anna F. Dominiczak,Alison M. Dunning,Douglas F. Easton,Charles B. Eaton,Paul Elliott,Evangelos Evangelou,Jessica D. Faul,Tatiana Foroud,Alison Goate,Jian Gong,Hans J. Grabe,Jeffrey Haessler,Christopher A. Haiman,Göran Hallmans,Anke R. Hammerschlag,Sarah E. Harris,Andrew T. Hattersley,Andrew Heath,Chris Hsu,William G. Iacono,Stavroula Kanoni,Manav Kapoor,Jaakko Kaprio,Sharon L.R. Kardia,Fredrik Karpe,Jukka Kontto,Jaspal S. Kooner,Charles Kooperberg,Kari Kuulasmaa,Markku Laakso,Dongbing Lai,Claudia Langenberg,Nhung Le,Guillaume Lettre,Anu Loukola,Jian'an Luan,Pamela A. F. Madden,Massimo Mangino,Riccardo E. Marioni,Eirini Marouli,Jonathan Marten,Nicholas G. Martin,Matt McGue,Kyriaki Michailidou,Evelin Mihailov,Alireza Moayyeri,Marie Moitry,Martina Mueller-Nurasyid,Aliya Naheed,Matthias Nauck,Matt J. Neville,Sune F. Nielsen,Kari E. North,Markus Perola,Paul D.P. Pharoah,Giorgio Pistis,Tinca J. C. Polderman,Danielle Posthuma,Neil Poulter,Beenish Qaiser,Asif Rasheed,Alexander P. Reiner,Frida Renström,John P. Rice,Rebecca Rohde,Olov Rolandsson,Nilesh J. Samani,Maria Samuel,David Schlessinger,Steven Scholte,Robert A. Scott,Peter S. Sever,Yaming Shao,Nick Shrine,Jennifer A. Smith,John M. Starr,Kathleen Stirrups,Danielle Stram,Heather M. Stringham,Ioanna Tachmazidou,Jean-Claude Tardif,Deborah J. Thompson,Hilary A. Tindle,Vinicius Tragante,Stella Trompet,Valérie Turcot,Jessica Tyrrell,Ilonca Vaartjes,Andries R. van der Leij,Peter van der Meer,Tibor V. Varga,Niek Verweij,Henry Voelzke,Nicholas J. Wareham,Helen R. Warren,David R. Weir,Stefan Weiss,Leah Wetherill,Hanieh Yaghootkar,Ersin Yavas,Yu Jiang,Fang Chen,Xiaowei Zhan,Weihua Zhang,Wei Zhao,Kaixin Zhou,Philippe Amouyel,Stefan Blankenberg,Mark J. Caulfield,Rajiv Chowdhury,Francesco Cucca,Ian J. Deary,Panos Deloukas,Emanuele Di Angelantonio,Marco M Ferrario,Jean Ferrières,Paul W. Franks,Timothy M. Frayling,Philippe M. Frossard,Ian P. Hall,Caroline Hayward,Jan-Håkan Jansson,J. Wouter Jukema,Frank Kee,Satu Männistö,Andres Metspalu,Patricia B. Munroe,Børge G. Nordestgaard,Colin N. A. Palmer,Veikko Salomaa,Naveed Sattar,Tim D. Spector,David P. Strachan,Pim van der Harst,Eleftheria Zeggini,Danish Saleheen,Adam S. Butterworth,Louise V. Wain,Gonçalo R. Abecasis,John Danesh,Martin D. Tobin,Scott I. Vrieze,Dajiang J. Liu,Joanna M. M. Howson +174 more
TL;DR: In this article, a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants) was performed to investigate the association of SNVs with smoking behavior traits.
Journal ArticleDOI
The effect of corn straw return on corn production in Northeast China: An integrated regional evaluation with meta-analysis and system dynamics
TL;DR: Wang et al. as discussed by the authors studied the effects of corn straw return on corn yield increase with meta-analysis, and they concluded that the optimal amount of straw return is 48% of the corn straw, which brings 5.83% increase in corn yield.
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Tolerance of Listeria monocytogenes to biocides used in food processing environments.
TL;DR: In this article, the authors discuss the current literature on the ability of L monocytogenes strains to tolerate biocides especially quaternary ammonium compounds as well as the mechanisms of tolerance towards Biocides including the activation of efflux pump systems.
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Struan F.A. Grant,Gudmar Thorleifsson,Inga Reynisdottir,Rafil Benediktsson,Andrei Manolescu,Jesus Sainz,Agnar Helgason,Hreinn Stefansson,Valur Emilsson,Anna Helgadottir,Unnur Styrkarsdottir,Kristinn P. Magnusson,G. Bragi Walters,Ebba Palsdottir,Thorbjorg Jonsdottir,Thorunn Gudmundsdottir,Arnaldur Gylfason,Jona Saemundsdottir,Robert L. Wilensky,Muredach P. Reilly,Daniel J. Rader,Yu Z. Bagger,Claus Christiansen,Vilmundur Gudnason,Gunnar Sigurdsson,Unnur Thorsteinsdottir,Jeffrey R. Gulcher,Augustine Kong,Kari Stefansson +28 more
TL;DR: A microsatellite within intron 3 of the transcription factor 7–like 2 gene (TCF7L2; formerly TCF4) was associated with type 2 diabetes mellitus and is thought to act through regulation of proglucagon gene expression in enteroendocrine cells via the Wnt signaling pathway.
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