Literature DB >> 25961943

The impact of low-frequency and rare variants on lipid levels.

Ida Surakka1, Momoko Horikoshi2, Reedik Mägi3, Antti-Pekka Sarin1, Anubha Mahajan4, Vasiliki Lagou2, Letizia Marullo5, Teresa Ferreira4, Benjamin Miraglio6, Sanna Timonen6, Johannes Kettunen1, Matti Pirinen6, Juha Karjalainen7, Gudmar Thorleifsson8, Sara Hägg9, Jouke-Jan Hottenga10, Aaron Isaacs11, Claes Ladenvall12, Marian Beekman13, Tõnu Esko14, Janina S Ried15, Christopher P Nelson16, Christina Willenborg17, Stefan Gustafsson9, Harm-Jan Westra7, Matthew Blades18, Anton J M de Craen19, Eco J de Geus10, Joris Deelen13, Harald Grallert20, Anders Hamsten21, Aki S Havulinna22, Christian Hengstenberg23, Jeanine J Houwing-Duistermaat24, Elina Hyppönen25, Lennart C Karssen26, Terho Lehtimäki27, Valeriya Lyssenko28, Patrik K E Magnusson29, Evelin Mihailov3, Martina Müller-Nurasyid30, John-Patrick Mpindi6, Nancy L Pedersen29, Brenda W J H Penninx31, Markus Perola32, Tune H Pers33, Annette Peters34, Johan Rung35, Johannes H Smit31, Valgerdur Steinthorsdottir8, Martin D Tobin36, Natalia Tsernikova3, Elisabeth M van Leeuwen26, Jorma S Viikari37, Sara M Willems26, Gonneke Willemsen10, Heribert Schunkert23, Jeanette Erdmann17, Nilesh J Samani16, Jaakko Kaprio38, Lars Lind39, Christian Gieger40, Andres Metspalu41, P Eline Slagboom13, Leif Groop42, Cornelia M van Duijn11, Johan G Eriksson43, Antti Jula22, Veikko Salomaa22, Dorret I Boomsma10, Christine Power44, Olli T Raitakari45, Erik Ingelsson46, Marjo-Riitta Järvelin47, Unnur Thorsteinsdottir48, Lude Franke7, Elina Ikonen49, Olli Kallioniemi6, Vilja Pietiäinen6, Cecilia M Lindgren50, Kari Stefansson48, Aarno Palotie51, Mark I McCarthy52, Andrew P Morris53, Inga Prokopenko54, Samuli Ripatti55.   

Abstract

Using a genome-wide screen of 9.6 million genetic variants achieved through 1000 Genomes Project imputation in 62,166 samples, we identify association to lipid traits in 93 loci, including 79 previously identified loci with new lead SNPs and 10 new loci, 15 loci with a low-frequency lead SNP and 10 loci with a missense lead SNP, and 2 loci with an accumulation of rare variants. In six loci, SNPs with established function in lipid genetics (CELSR2, GCKR, LIPC and APOE) or candidate missense mutations with predicted damaging function (CD300LG and TM6SF2) explained the locus associations. The low-frequency variants increased the proportion of variance explained, particularly for low-density lipoprotein cholesterol and total cholesterol. Altogether, our results highlight the impact of low-frequency variants in complex traits and show that imputation offers a cost-effective alternative to resequencing.

Entities:  

Mesh：

Year:  2015        PMID： 25961943      PMCID： PMC4757735          DOI： 10.1038/ng.3300

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


  42 in total

1.  Cloning of the novel gene TM6SF1 reveals conservation of clusters of paralogous genes between human chromosomes 15q24-->q26 and 19p13.3-->p12.

Authors:  L Carim-Todd; M Escarceller; X Estivill; L Sumoy
Journal:  Cytogenet Cell Genet       Date:  2000

2.  GCTA: a tool for genome-wide complex trait analysis.

Authors:  Jian Yang; S Hong Lee; Michael E Goddard; Peter M Visscher
Journal:  Am J Hum Genet       Date:  2010-12-17       Impact factor: 11.025

3.  Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia.

Authors:  Christopher T Johansen; Jian Wang; Matthew B Lanktree; Henian Cao; Adam D McIntyre; Matthew R Ban; Rebecca A Martins; Brooke A Kennedy; Reina G Hassell; Maartje E Visser; Stephen M Schwartz; Benjamin F Voight; Roberto Elosua; Veikko Salomaa; Christopher J O'Donnell; Geesje M Dallinga-Thie; Sonia S Anand; Salim Yusuf; Murray W Huff; Sekar Kathiresan; Robert A Hegele
Journal:  Nat Genet       Date:  2010-07-25       Impact factor: 38.330

4.  Nepmucin/CLM-9, an Ig domain-containing sialomucin in vascular endothelial cells, promotes lymphocyte transendothelial migration in vitro.

Authors:  Soojung Jin; Eiji Umemoto; Toshiyuki Tanaka; Yoshimitsu Shimomura; Kazuo Tohya; Keiji Kunizawa; Bo-Gie Yang; Myoung Ho Jang; Takako Hirata; Masayuki Miyasaka
Journal:  FEBS Lett       Date:  2008-08-04       Impact factor: 4.124

5.  GWAMA: software for genome-wide association meta-analysis.

Authors:  Reedik Mägi; Andrew P Morris
Journal:  BMC Bioinformatics       Date:  2010-05-28       Impact factor: 3.169

6.  A method and server for predicting damaging missense mutations.

Authors:  Ivan A Adzhubei; Steffen Schmidt; Leonid Peshkin; Vasily E Ramensky; Anna Gerasimova; Peer Bork; Alexey S Kondrashov; Shamil R Sunyaev
Journal:  Nat Methods       Date:  2010-04       Impact factor: 28.547

7.  Meta-analysis of sex-specific genome-wide association studies.

Authors:  Reedik Magi; Cecilia M Lindgren; Andrew P Morris
Journal:  Genet Epidemiol       Date:  2010-12       Impact factor: 2.135

8.  Biological, clinical and population relevance of 95 loci for blood lipids.

Authors:  Tanya M Teslovich; Kiran Musunuru; Albert V Smith; Andrew C Edmondson; Ioannis M Stylianou; Masahiro Koseki; James P Pirruccello; Samuli Ripatti; Daniel I Chasman; Cristen J Willer; Christopher T Johansen; Sigrid W Fouchier; Aaron Isaacs; Gina M Peloso; Maja Barbalic; Sally L Ricketts; Joshua C Bis; Yurii S Aulchenko; Gudmar Thorleifsson; Mary F Feitosa; John Chambers; Marju Orho-Melander; Olle Melander; Toby Johnson; Xiaohui Li; Xiuqing Guo; Mingyao Li; Yoon Shin Cho; Min Jin Go; Young Jin Kim; Jong-Young Lee; Taesung Park; Kyunga Kim; Xueling Sim; Rick Twee-Hee Ong; Damien C Croteau-Chonka; Leslie A Lange; Joshua D Smith; Kijoung Song; Jing Hua Zhao; Xin Yuan; Jian'an Luan; Claudia Lamina; Andreas Ziegler; Weihua Zhang; Robert Y L Zee; Alan F Wright; Jacqueline C M Witteman; James F Wilson; Gonneke Willemsen; H-Erich Wichmann; John B Whitfield; Dawn M Waterworth; Nicholas J Wareham; Gérard Waeber; Peter Vollenweider; Benjamin F Voight; Veronique Vitart; Andre G Uitterlinden; Manuela Uda; Jaakko Tuomilehto; John R Thompson; Toshiko Tanaka; Ida Surakka; Heather M Stringham; Tim D Spector; Nicole Soranzo; Johannes H Smit; Juha Sinisalo; Kaisa Silander; Eric J G Sijbrands; Angelo Scuteri; James Scott; David Schlessinger; Serena Sanna; Veikko Salomaa; Juha Saharinen; Chiara Sabatti; Aimo Ruokonen; Igor Rudan; Lynda M Rose; Robert Roberts; Mark Rieder; Bruce M Psaty; Peter P Pramstaller; Irene Pichler; Markus Perola; Brenda W J H Penninx; Nancy L Pedersen; Cristian Pattaro; Alex N Parker; Guillaume Pare; Ben A Oostra; Christopher J O'Donnell; Markku S Nieminen; Deborah A Nickerson; Grant W Montgomery; Thomas Meitinger; Ruth McPherson; Mark I McCarthy; Wendy McArdle; David Masson; Nicholas G Martin; Fabio Marroni; Massimo Mangino; Patrik K E Magnusson; Gavin Lucas; Robert Luben; Ruth J F Loos; Marja-Liisa Lokki; Guillaume Lettre; Claudia Langenberg; Lenore J Launer; Edward G Lakatta; Reijo Laaksonen; Kirsten O Kyvik; Florian Kronenberg; Inke R König; Kay-Tee Khaw; Jaakko Kaprio; Lee M Kaplan; Asa Johansson; Marjo-Riitta Jarvelin; A Cecile J W Janssens; Erik Ingelsson; Wilmar Igl; G Kees Hovingh; Jouke-Jan Hottenga; Albert Hofman; Andrew A Hicks; Christian Hengstenberg; Iris M Heid; Caroline Hayward; Aki S Havulinna; Nicholas D Hastie; Tamara B Harris; Talin Haritunians; Alistair S Hall; Ulf Gyllensten; Candace Guiducci; Leif C Groop; Elena Gonzalez; Christian Gieger; Nelson B Freimer; Luigi Ferrucci; Jeanette Erdmann; Paul Elliott; Kenechi G Ejebe; Angela Döring; Anna F Dominiczak; Serkalem Demissie; Panagiotis Deloukas; Eco J C de Geus; Ulf de Faire; Gabriel Crawford; Francis S Collins; Yii-der I Chen; Mark J Caulfield; Harry Campbell; Noel P Burtt; Lori L Bonnycastle; Dorret I Boomsma; S Matthijs Boekholdt; Richard N Bergman; Inês Barroso; Stefania Bandinelli; Christie M Ballantyne; Themistocles L Assimes; Thomas Quertermous; David Altshuler; Mark Seielstad; Tien Y Wong; E-Shyong Tai; Alan B Feranil; Christopher W Kuzawa; Linda S Adair; Herman A Taylor; Ingrid B Borecki; Stacey B Gabriel; James G Wilson; Hilma Holm; Unnur Thorsteinsdottir; Vilmundur Gudnason; Ronald M Krauss; Karen L Mohlke; Jose M Ordovas; Patricia B Munroe; Jaspal S Kooner; Alan R Tall; Robert A Hegele; John J P Kastelein; Eric E Schadt; Jerome I Rotter; Eric Boerwinkle; David P Strachan; Vincent Mooser; Kari Stefansson; Muredach P Reilly; Nilesh J Samani; Heribert Schunkert; L Adrienne Cupples; Manjinder S Sandhu; Paul M Ridker; Daniel J Rader; Cornelia M van Duijn; Leena Peltonen; Gonçalo R Abecasis; Michael Boehnke; Sekar Kathiresan
Journal:  Nature       Date:  2010-08-05       Impact factor: 49.962

9.  The P446L variant in GCKR associated with fasting plasma glucose and triglyceride levels exerts its effect through increased glucokinase activity in liver.

Authors:  Nicola L Beer; Nicholas D Tribble; Laura J McCulloch; Charlotta Roos; Paul R V Johnson; Marju Orho-Melander; Anna L Gloyn
Journal:  Hum Mol Genet       Date:  2009-07-30       Impact factor: 6.150

10.  New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Authors:  Josée Dupuis; Claudia Langenberg; Inga Prokopenko; Richa Saxena; Nicole Soranzo; Anne U Jackson; Eleanor Wheeler; Nicole L Glazer; Nabila Bouatia-Naji; Anna L Gloyn; Cecilia M Lindgren; Reedik Mägi; Andrew P Morris; Joshua Randall; Toby Johnson; Paul Elliott; Denis Rybin; Gudmar Thorleifsson; Valgerdur Steinthorsdottir; Peter Henneman; Harald Grallert; Abbas Dehghan; Jouke Jan Hottenga; Christopher S Franklin; Pau Navarro; Kijoung Song; Anuj Goel; John R B Perry; Josephine M Egan; Taina Lajunen; Niels Grarup; Thomas Sparsø; Alex Doney; Benjamin F Voight; Heather M Stringham; Man Li; Stavroula Kanoni; Peter Shrader; Christine Cavalcanti-Proença; Meena Kumari; Lu Qi; Nicholas J Timpson; Christian Gieger; Carina Zabena; Ghislain Rocheleau; Erik Ingelsson; Ping An; Jeffrey O'Connell; Jian'an Luan; Amanda Elliott; Steven A McCarroll; Felicity Payne; Rosa Maria Roccasecca; François Pattou; Praveen Sethupathy; Kristin Ardlie; Yavuz Ariyurek; Beverley Balkau; Philip Barter; John P Beilby; Yoav Ben-Shlomo; Rafn Benediktsson; Amanda J Bennett; Sven Bergmann; Murielle Bochud; Eric Boerwinkle; Amélie Bonnefond; Lori L Bonnycastle; Knut Borch-Johnsen; Yvonne Böttcher; Eric Brunner; Suzannah J Bumpstead; Guillaume Charpentier; Yii-Der Ida Chen; Peter Chines; Robert Clarke; Lachlan J M Coin; Matthew N Cooper; Marilyn Cornelis; Gabe Crawford; Laura Crisponi; Ian N M Day; Eco J C de Geus; Jerome Delplanque; Christian Dina; Michael R Erdos; Annette C Fedson; Antje Fischer-Rosinsky; Nita G Forouhi; Caroline S Fox; Rune Frants; Maria Grazia Franzosi; Pilar Galan; Mark O Goodarzi; Jürgen Graessler; Christopher J Groves; Scott Grundy; Rhian Gwilliam; Ulf Gyllensten; Samy Hadjadj; Göran Hallmans; Naomi Hammond; Xijing Han; Anna-Liisa Hartikainen; Neelam Hassanali; Caroline Hayward; Simon C Heath; Serge Hercberg; Christian Herder; Andrew A Hicks; David R Hillman; Aroon D Hingorani; Albert Hofman; Jennie Hui; Joe Hung; Bo Isomaa; Paul R V Johnson; Torben Jørgensen; Antti Jula; Marika Kaakinen; Jaakko Kaprio; Y Antero Kesaniemi; Mika Kivimaki; Beatrice Knight; Seppo Koskinen; Peter Kovacs; Kirsten Ohm Kyvik; G Mark Lathrop; Debbie A Lawlor; Olivier Le Bacquer; Cécile Lecoeur; Yun Li; Valeriya Lyssenko; Robert Mahley; Massimo Mangino; Alisa K Manning; María Teresa Martínez-Larrad; Jarred B McAteer; Laura J McCulloch; Ruth McPherson; Christa Meisinger; David Melzer; David Meyre; Braxton D Mitchell; Mario A Morken; Sutapa Mukherjee; Silvia Naitza; Narisu Narisu; Matthew J Neville; Ben A Oostra; Marco Orrù; Ruth Pakyz; Colin N A Palmer; Giuseppe Paolisso; Cristian Pattaro; Daniel Pearson; John F Peden; Nancy L Pedersen; Markus Perola; Andreas F H Pfeiffer; Irene Pichler; Ozren Polasek; Danielle Posthuma; Simon C Potter; Anneli Pouta; Michael A Province; Bruce M Psaty; Wolfgang Rathmann; Nigel W Rayner; Kenneth Rice; Samuli Ripatti; Fernando Rivadeneira; Michael Roden; Olov Rolandsson; Annelli Sandbaek; Manjinder Sandhu; Serena Sanna; Avan Aihie Sayer; Paul Scheet; Laura J Scott; Udo Seedorf; Stephen J Sharp; Beverley Shields; Gunnar Sigurethsson; Eric J G Sijbrands; Angela Silveira; Laila Simpson; Andrew Singleton; Nicholas L Smith; Ulla Sovio; Amy Swift; Holly Syddall; Ann-Christine Syvänen; Toshiko Tanaka; Barbara Thorand; Jean Tichet; Anke Tönjes; Tiinamaija Tuomi; André G Uitterlinden; Ko Willems van Dijk; Mandy van Hoek; Dhiraj Varma; Sophie Visvikis-Siest; Veronique Vitart; Nicole Vogelzangs; Gérard Waeber; Peter J Wagner; Andrew Walley; G Bragi Walters; Kim L Ward; Hugh Watkins; Michael N Weedon; Sarah H Wild; Gonneke Willemsen; Jaqueline C M Witteman; John W G Yarnell; Eleftheria Zeggini; Diana Zelenika; Björn Zethelius; Guangju Zhai; Jing Hua Zhao; M Carola Zillikens; Ingrid B Borecki; Ruth J F Loos; Pierre Meneton; Patrik K E Magnusson; David M Nathan; Gordon H Williams; Andrew T Hattersley; Kaisa Silander; Veikko Salomaa; George Davey Smith; Stefan R Bornstein; Peter Schwarz; Joachim Spranger; Fredrik Karpe; Alan R Shuldiner; Cyrus Cooper; George V Dedoussis; Manuel Serrano-Ríos; Andrew D Morris; Lars Lind; Lyle J Palmer; Frank B Hu; Paul W Franks; Shah Ebrahim; Michael Marmot; W H Linda Kao; James S Pankow; Michael J Sampson; Johanna Kuusisto; Markku Laakso; Torben Hansen; Oluf Pedersen; Peter Paul Pramstaller; H Erich Wichmann; Thomas Illig; Igor Rudan; Alan F Wright; Michael Stumvoll; Harry Campbell; James F Wilson; Richard N Bergman; Thomas A Buchanan; Francis S Collins; Karen L Mohlke; Jaakko Tuomilehto; Timo T Valle; David Altshuler; Jerome I Rotter; David S Siscovick; Brenda W J H Penninx; Dorret I Boomsma; Panos Deloukas; Timothy D Spector; Timothy M Frayling; Luigi Ferrucci; Augustine Kong; Unnur Thorsteinsdottir; Kari Stefansson; Cornelia M van Duijn; Yurii S Aulchenko; Antonio Cao; Angelo Scuteri; David Schlessinger; Manuela Uda; Aimo Ruokonen; Marjo-Riitta Jarvelin; Dawn M Waterworth; Peter Vollenweider; Leena Peltonen; Vincent Mooser; Goncalo R Abecasis; Nicholas J Wareham; Robert Sladek; Philippe Froguel; Richard M Watanabe; James B Meigs; Leif Groop; Michael Boehnke; Mark I McCarthy; Jose C Florez; Inês Barroso
Journal:  Nat Genet       Date:  2010-01-17       Impact factor: 38.330
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  168 in total

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Authors:  Dilek Pirim; Xingbin Wang; Vipavee Niemsiri; Zaheda H Radwan; Clareann H Bunker; John E Hokanson; Richard F Hamman; M Michael Barmada; F Yesim Demirci; M Ilyas Kamboh
Journal:  Metabolism       Date:  2015-09-30       Impact factor: 8.694

3.  Metabolic enzymes expressed by cancer cells impact the immune infiltrate.

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Journal:  Oncoimmunology       Date:  2019-03-30       Impact factor: 8.110

4.  Shared genetic architecture between metabolic traits and Alzheimer's disease: a large-scale genome-wide cross-trait analysis.

Authors:  Zhaozhong Zhu; Yifei Lin; Xihao Li; Jane A Driver; Liming Liang
Journal:  Hum Genet       Date:  2019-02-25       Impact factor: 4.132

5.  Association analyses based on false discovery rate implicate new loci for coronary artery disease.

Authors:  Christopher P Nelson; Anuj Goel; Adam S Butterworth; Stavroula Kanoni; Tom R Webb; Eirini Marouli; Lingyao Zeng; Ioanna Ntalla; Florence Y Lai; Jemma C Hopewell; Olga Giannakopoulou; Tao Jiang; Stephen E Hamby; Emanuele Di Angelantonio; Themistocles L Assimes; Erwin P Bottinger; John C Chambers; Robert Clarke; Colin N A Palmer; Richard M Cubbon; Patrick Ellinor; Raili Ermel; Evangelos Evangelou; Paul W Franks; Christopher Grace; Dongfeng Gu; Aroon D Hingorani; Joanna M M Howson; Erik Ingelsson; Adnan Kastrati; Thorsten Kessler; Theodosios Kyriakou; Terho Lehtimäki; Xiangfeng Lu; Yingchang Lu; Winfried März; Ruth McPherson; Andres Metspalu; Mar Pujades-Rodriguez; Arno Ruusalepp; Eric E Schadt; Amand F Schmidt; Michael J Sweeting; Pierre A Zalloua; Kamal AlGhalayini; Bernard D Keavney; Jaspal S Kooner; Ruth J F Loos; Riyaz S Patel; Martin K Rutter; Maciej Tomaszewski; Ioanna Tzoulaki; Eleftheria Zeggini; Jeanette Erdmann; George Dedoussis; Johan L M Björkegren; Heribert Schunkert; Martin Farrall; John Danesh; Nilesh J Samani; Hugh Watkins; Panos Deloukas
Journal:  Nat Genet       Date:  2017-07-17       Impact factor: 38.330

6.  Methods for meta-analysis of multiple traits using GWAS summary statistics.

Authors:  Debashree Ray; Michael Boehnke
Journal:  Genet Epidemiol       Date:  2017-12-10       Impact factor: 2.135

7.  Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases.

Authors:  Masahiro Kanai; Masato Akiyama; Atsushi Takahashi; Nana Matoba; Yukihide Momozawa; Masashi Ikeda; Nakao Iwata; Shiro Ikegawa; Makoto Hirata; Koichi Matsuda; Michiaki Kubo; Yukinori Okada; Yoichiro Kamatani
Journal:  Nat Genet       Date:  2018-02-05       Impact factor: 38.330

Review 8.  Drug development in the era of precision medicine.

Authors:  Sarah A Dugger; Adam Platt; David B Goldstein
Journal:  Nat Rev Drug Discov       Date:  2017-12-08       Impact factor: 84.694

9.  Directional ABCA1-mediated cholesterol efflux and apoB-lipoprotein secretion in the retinal pigment epithelium.

Authors:  Nicholas N Lyssenko; Naqi Haider; Antonino Picataggi; Eleonora Cipollari; Wanzhen Jiao; Michael C Phillips; Daniel J Rader; Venkata Ramana Murthy Chavali
Journal:  J Lipid Res       Date:  2018-08-03       Impact factor: 5.922

10.  Interactions Between Regulatory Variants in CYP7A1 (Cholesterol 7α-Hydroxylase) Promoter and Enhancer Regions Regulate CYP7A1 Expression.

Authors:  Danxin Wang; Katherine Hartmann; Michal Seweryn; Wolfgang Sadee
Journal:  Circ Genom Precis Med       Date:  2018-10
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