Literature DB >> 24395754

QCGWAS: A flexible R package for automated quality control of genome-wide association results.

Peter J van der Most1, Ahmad Vaez1, Bram P Prins2, M Loretto Munoz1, Harold Snieder1, Behrooz Z Alizadeh1, Ilja M Nolte1.   

Abstract

QCGWAS is an R package that automates the quality control of genome-wide association result files. Its main purpose is to facilitate the quality control of a large number of such files before meta-analysis. Alternatively, it can be used by individual cohorts to check their own result files. QCGWAS is flexible and has a wide range of options, allowing rapid generation of high-quality input files for meta-analysis of genome-wide association studies. AVAILABILITY: http://cran.r-project.org/web/packages/QCGWAS CONTACT: i.m.nolte@umcg.nl Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mesh：

Year:  2014        PMID： 24395754     DOI： 10.1093/bioinformatics/btt745

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

Review 1.  Genome-wide association studies in nephrology: using known associations for data checks.

Authors:  Matthias Wuttke; Franz Schaefer; Craig S Wong; Anna Köttgen
Journal:  Am J Kidney Dis       Date:  2014-11-18       Impact factor: 8.860

2.  Genome-wide meta-analyses reveal novel loci for verbal short-term memory and learning.

Authors:  Jari Lahti; Samuli Tuominen; Qiong Yang; Giulio Pergola; Shahzad Ahmad; Najaf Amin; Nicola J Armstrong; Alexa Beiser; Katharina Bey; Joshua C Bis; Eric Boerwinkle; Jan Bressler; Archie Campbell; Harry Campbell; Qiang Chen; Janie Corley; Simon R Cox; Gail Davies; Philip L De Jager; Eske M Derks; Jessica D Faul; Annette L Fitzpatrick; Alison E Fohner; Ian Ford; Myriam Fornage; Zachary Gerring; Hans J Grabe; Francine Grodstein; Vilmundur Gudnason; Eleanor Simonsick; Elizabeth G Holliday; Peter K Joshi; Eero Kajantie; Jaakko Kaprio; Pauliina Karell; Luca Kleineidam; Maria J Knol; Nicole A Kochan; John B Kwok; Markus Leber; Max Lam; Teresa Lee; Shuo Li; Anu Loukola; Tobias Luck; Riccardo E Marioni; Karen A Mather; Sarah Medland; Saira S Mirza; Mike A Nalls; Kwangsik Nho; Adrienne O'Donnell; Christopher Oldmeadow; Jodie Painter; Alison Pattie; Simone Reppermund; Shannon L Risacher; Richard J Rose; Vijay Sadashivaiah; Markus Scholz; Claudia L Satizabal; Peter W Schofield; Katharina E Schraut; Rodney J Scott; Jeannette Simino; Albert V Smith; Jennifer A Smith; David J Stott; Ida Surakka; Alexander Teumer; Anbupalam Thalamuthu; Stella Trompet; Stephen T Turner; Sven J van der Lee; Arno Villringer; Uwe Völker; Robert S Wilson; Katharina Wittfeld; Eero Vuoksimaa; Rui Xia; Kristine Yaffe; Lei Yu; Habil Zare; Wei Zhao; David Ames; John Attia; David A Bennett; Henry Brodaty; Daniel I Chasman; Aaron L Goldman; Caroline Hayward; M Arfan Ikram; J Wouter Jukema; Sharon L R Kardia; Todd Lencz; Markus Loeffler; Venkata S Mattay; Aarno Palotie; Bruce M Psaty; Alfredo Ramirez; Paul M Ridker; Steffi G Riedel-Heller; Perminder S Sachdev; Andrew J Saykin; Martin Scherer; Peter R Schofield; Stephen Sidney; John M Starr; Julian Trollor; William Ulrich; Michael Wagner; David R Weir; James F Wilson; Margaret J Wright; Daniel R Weinberger; Stephanie Debette; Johan G Eriksson; Thomas H Mosley; Lenore J Launer; Cornelia M van Duijn; Ian J Deary; Sudha Seshadri; Katri Räikkönen
Journal:  Mol Psychiatry       Date:  2022-08-16       Impact factor: 13.437

3.  Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

Authors:  Nicola Barban; Rick Jansen; Ronald de Vlaming; Ahmad Vaez; Jornt J Mandemakers; Felix C Tropf; Xia Shen; James F Wilson; Daniel I Chasman; Ilja M Nolte; Vinicius Tragante; Sander W van der Laan; John R B Perry; Augustine Kong; Tarunveer S Ahluwalia; Eva Albrecht; Laura Yerges-Armstrong; Gil Atzmon; Kirsi Auro; Kristin Ayers; Andrew Bakshi; Danny Ben-Avraham; Klaus Berger; Aviv Bergman; Lars Bertram; Lawrence F Bielak; Gyda Bjornsdottir; Marc Jan Bonder; Linda Broer; Minh Bui; Caterina Barbieri; Alana Cavadino; Jorge E Chavarro; Constance Turman; Maria Pina Concas; Heather J Cordell; Gail Davies; Peter Eibich; Nicholas Eriksson; Tõnu Esko; Joel Eriksson; Fahimeh Falahi; Janine F Felix; Mark Alan Fontana; Lude Franke; Ilaria Gandin; Audrey J Gaskins; Christian Gieger; Erica P Gunderson; Xiuqing Guo; Caroline Hayward; Chunyan He; Edith Hofer; Hongyan Huang; Peter K Joshi; Stavroula Kanoni; Robert Karlsson; Stefan Kiechl; Annette Kifley; Alexander Kluttig; Peter Kraft; Vasiliki Lagou; Cecile Lecoeur; Jari Lahti; Ruifang Li-Gao; Penelope A Lind; Tian Liu; Enes Makalic; Crysovalanto Mamasoula; Lindsay Matteson; Hamdi Mbarek; Patrick F McArdle; George McMahon; S Fleur W Meddens; Evelin Mihailov; Mike Miller; Stacey A Missmer; Claire Monnereau; Peter J van der Most; Ronny Myhre; Mike A Nalls; Teresa Nutile; Ioanna Panagiota Kalafati; Eleonora Porcu; Inga Prokopenko; Kumar B Rajan; Janet Rich-Edwards; Cornelius A Rietveld; Antonietta Robino; Lynda M Rose; Rico Rueedi; Kathleen A Ryan; Yasaman Saba; Daniel Schmidt; Jennifer A Smith; Lisette Stolk; Elizabeth Streeten; Anke Tönjes; Gudmar Thorleifsson; Sheila Ulivi; Juho Wedenoja; Juergen Wellmann; Peter Willeit; Jie Yao; Loic Yengo; Jing Hua Zhao; Wei Zhao; Daria V Zhernakova; Najaf Amin; Howard Andrews; Beverley Balkau; Nir Barzilai; Sven Bergmann; Ginevra Biino; Hans Bisgaard; Klaus Bønnelykke; Dorret I Boomsma; Julie E Buring; Harry Campbell; Stefania Cappellani; Marina Ciullo; Simon R Cox; Francesco Cucca; Daniela Toniolo; George Davey-Smith; Ian J Deary; George Dedoussis; Panos Deloukas; Cornelia M van Duijn; Eco J C de Geus; Johan G Eriksson; Denis A Evans; Jessica D Faul; Cinzia Felicita Sala; Philippe Froguel; Paolo Gasparini; Giorgia Girotto; Hans-Jörgen Grabe; Karin Halina Greiser; Patrick J F Groenen; Hugoline G de Haan; Johannes Haerting; Tamara B Harris; Andrew C Heath; Kauko Heikkilä; Albert Hofman; Georg Homuth; Elizabeth G Holliday; John Hopper; Elina Hyppönen; Bo Jacobsson; Vincent W V Jaddoe; Magnus Johannesson; Astanand Jugessur; Mika Kähönen; Eero Kajantie; Sharon L R Kardia; Bernard Keavney; Ivana Kolcic; Päivikki Koponen; Peter Kovacs; Florian Kronenberg; Zoltan Kutalik; Martina La Bianca; Genevieve Lachance; William G Iacono; Sandra Lai; Terho Lehtimäki; David C Liewald; Cecilia M Lindgren; Yongmei Liu; Robert Luben; Michael Lucht; Riitta Luoto; Per Magnus; Patrik K E Magnusson; Nicholas G Martin; Matt McGue; Ruth McQuillan; Sarah E Medland; Christa Meisinger; Dan Mellström; Andres Metspalu; Michela Traglia; Lili Milani; Paul Mitchell; Grant W Montgomery; Dennis Mook-Kanamori; Renée de Mutsert; Ellen A Nohr; Claes Ohlsson; Jørn Olsen; Ken K Ong; Lavinia Paternoster; Alison Pattie; Brenda W J H Penninx; Markus Perola; Patricia A Peyser; Mario Pirastu; Ozren Polasek; Chris Power; Jaakko Kaprio; Leslie J Raffel; Katri Räikkönen; Olli Raitakari; Paul M Ridker; Susan M Ring; Kathryn Roll; Igor Rudan; Daniela Ruggiero; Dan Rujescu; Veikko Salomaa; David Schlessinger; Helena Schmidt; Reinhold Schmidt; Nicole Schupf; Johannes Smit; Rossella Sorice; Tim D Spector; John M Starr; Doris Stöckl; Konstantin Strauch; Michael Stumvoll; Morris A Swertz; Unnur Thorsteinsdottir; A Roy Thurik; Nicholas J Timpson; Joyce Y Tung; André G Uitterlinden; Simona Vaccargiu; Jorma Viikari; Veronique Vitart; Henry Völzke; Peter Vollenweider; Dragana Vuckovic; Johannes Waage; Gert G Wagner; Jie Jin Wang; Nicholas J Wareham; David R Weir; Gonneke Willemsen; Johann Willeit; Alan F Wright; Krina T Zondervan; Kari Stefansson; Robert F Krueger; James J Lee; Daniel J Benjamin; David Cesarini; Philipp D Koellinger; Marcel den Hoed; Harold Snieder; Melinda C Mills
Journal:  Nat Genet       Date:  2016-10-31       Impact factor: 38.330

4.  Genome-wide association study of circulating interleukin 6 levels identifies novel loci.

Authors:  Tarunveer S Ahluwalia; Bram P Prins; Mohammadreza Abdollahi; Nicola J Armstrong; Stella Aslibekyan; Lisa Bain; Barbara Jefferis; Jens Baumert; Marian Beekman; Yoav Ben-Shlomo; Joshua C Bis; Braxton D Mitchell; Eco de Geus; Graciela E Delgado; Diana Marek; Joel Eriksson; Eero Kajantie; Stavroula Kanoni; John P Kemp; Chen Lu; Riccardo E Marioni; Stela McLachlan; Yuri Milaneschi; Ilja M Nolte; Alexandros M Petrelis; Eleonora Porcu; Maria Sabater-Lleal; Elnaz Naderi; Ilkka Seppälä; Tina Shah; Gaurav Singhal; Marie Standl; Alexander Teumer; Anbupalam Thalamuthu; Elisabeth Thiering; Stella Trompet; Christie M Ballantyne; Emelia J Benjamin; Juan P Casas; Catherine Toben; George Dedoussis; Joris Deelen; Peter Durda; Jorgen Engmann; Mary F Feitosa; Harald Grallert; Ann Hammarstedt; Sarah E Harris; Georg Homuth; Jouke-Jan Hottenga; Sirpa Jalkanen; Yalda Jamshidi; Magdalene C Jawahar; Tine Jess; Mika Kivimaki; Marcus E Kleber; Jari Lahti; Yongmei Liu; Pedro Marques-Vidal; Dan Mellström; Simon P Mooijaart; Martina Müller-Nurasyid; Brenda Penninx; Joana A Revez; Peter Rossing; Katri Räikkönen; Naveed Sattar; Hubert Scharnagl; Bengt Sennblad; Angela Silveira; Beate St Pourcain; Nicholas J Timpson; Julian Trollor; Jenny van Dongen; Diana Van Heemst; Sophie Visvikis-Siest; Peter Vollenweider; Uwe Völker; Melanie Waldenberger; Gonneke Willemsen; Delilah Zabaneh; Richard W Morris; Donna K Arnett; Bernhard T Baune; Dorret I Boomsma; Yen-Pei C Chang; Ian J Deary; Panos Deloukas; Johan G Eriksson; David M Evans; Manuel A Ferreira; Tom Gaunt; Vilmundur Gudnason; Anders Hamsten; Joachim Heinrich; Aroon Hingorani; Steve E Humphries; J Wouter Jukema; Wolfgang Koenig; Meena Kumari; Zoltan Kutalik; Deborah A Lawlor; Terho Lehtimäki; Winfried März; Karen A Mather; Silvia Naitza; Matthias Nauck; Claes Ohlsson; Jackie F Price; Olli Raitakari; Ken Rice; Perminder S Sachdev; Eline Slagboom; Thorkild I A Sørensen; Tim Spector; David Stacey; Maria G Stathopoulou; Toshiko Tanaka; S Goya Wannamethee; Peter Whincup; Jerome I Rotter; Abbas Dehghan; Eric Boerwinkle; Bruce M Psaty; Harold Snieder; Behrooz Z Alizadeh
Journal:  Hum Mol Genet       Date:  2021-04-27       Impact factor: 6.150

5.  Automated quality control for genome wide association studies.

Authors:  Sally R Ellingson; David W Fardo
Journal:  F1000Res       Date:  2016-07-29

6.  SeqSQC: A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data.

Authors:  Qian Liu; Qiang Hu; Song Yao; Marilyn L Kwan; Janise M Roh; Hua Zhao; Christine B Ambrosone; Lawrence H Kushi; Song Liu; Qianqian Zhu
Journal:  Genomics Proteomics Bioinformatics       Date:  2019-04-05       Impact factor: 6.409

7.  GWASinspector: comprehensive quality control of genome-wide association study results.

Authors:  Alireza Ani; Peter J van der Most; Harold Snieder; Ahmad Vaez; Ilja M Nolte
Journal:  Bioinformatics       Date:  2021-01-08       Impact factor: 6.937

8.  BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data.

Authors:  Jan Christian Kässens; Lars Wienbrandt; David Ellinghaus
Journal:  Gigascience       Date:  2021-06-29       Impact factor: 6.524

9.  Robust Gene-Gene Interaction Analysis in Genome Wide Association Studies.

Authors:  Yongkang Kim; Taesung Park
Journal:  PLoS One       Date:  2015-08-12       Impact factor: 3.240

10.  Genetic loci associated with heart rate variability and their effects on cardiac disease risk.

Authors:  Ilja M Nolte; M Loretto Munoz; Vinicius Tragante; Azmeraw T Amare; Rick Jansen; Ahmad Vaez; Benedikt von der Heyde; Christy L Avery; Joshua C Bis; Bram Dierckx; Jenny van Dongen; Stephanie M Gogarten; Philippe Goyette; Jussi Hernesniemi; Ville Huikari; Shih-Jen Hwang; Deepali Jaju; Kathleen F Kerr; Alexander Kluttig; Bouwe P Krijthe; Jitender Kumar; Sander W van der Laan; Leo-Pekka Lyytikäinen; Adam X Maihofer; Arpi Minassian; Peter J van der Most; Martina Müller-Nurasyid; Michel Nivard; Erika Salvi; James D Stewart; Julian F Thayer; Niek Verweij; Andrew Wong; Delilah Zabaneh; Mohammad H Zafarmand; Abdel Abdellaoui; Sulayma Albarwani; Christine Albert; Alvaro Alonso; Foram Ashar; Juha Auvinen; Tomas Axelsson; Dewleen G Baker; Paul I W de Bakker; Matteo Barcella; Riad Bayoumi; Rob J Bieringa; Dorret Boomsma; Gabrielle Boucher; Annie R Britton; Ingrid Christophersen; Andrea Dietrich; George B Ehret; Patrick T Ellinor; Markku Eskola; Janine F Felix; John S Floras; Oscar H Franco; Peter Friberg; Maaike G J Gademan; Mark A Geyer; Vilmantas Giedraitis; Catharina A Hartman; Daiane Hemerich; Albert Hofman; Jouke-Jan Hottenga; Heikki Huikuri; Nina Hutri-Kähönen; Xavier Jouven; Juhani Junttila; Markus Juonala; Antti M Kiviniemi; Jan A Kors; Meena Kumari; Tatiana Kuznetsova; Cathy C Laurie; Joop D Lefrandt; Yong Li; Yun Li; Duanping Liao; Marian C Limacher; Henry J Lin; Cecilia M Lindgren; Steven A Lubitz; Anubha Mahajan; Barbara McKnight; Henriette Meyer Zu Schwabedissen; Yuri Milaneschi; Nina Mononen; Andrew P Morris; Mike A Nalls; Gerjan Navis; Melanie Neijts; Kjell Nikus; Kari E North; Daniel T O'Connor; Johan Ormel; Siegfried Perz; Annette Peters; Bruce M Psaty; Olli T Raitakari; Victoria B Risbrough; Moritz F Sinner; David Siscovick; Johannes H Smit; Nicholas L Smith; Elsayed Z Soliman; Nona Sotoodehnia; Jan A Staessen; Phyllis K Stein; Adrienne M Stilp; Katarzyna Stolarz-Skrzypek; Konstantin Strauch; Johan Sundström; Cees A Swenne; Ann-Christine Syvänen; Jean-Claude Tardif; Kent D Taylor; Alexander Teumer; Timothy A Thornton; Lesley E Tinker; André G Uitterlinden; Jessica van Setten; Andreas Voss; Melanie Waldenberger; Kirk C Wilhelmsen; Gonneke Willemsen; Quenna Wong; Zhu-Ming Zhang; Alan B Zonderman; Daniele Cusi; Michele K Evans; Halina K Greiser; Pim van der Harst; Mohammad Hassan; Erik Ingelsson; Marjo-Riitta Järvelin; Stefan Kääb; Mika Kähönen; Mika Kivimaki; Charles Kooperberg; Diana Kuh; Terho Lehtimäki; Lars Lind; Caroline M Nievergelt; Chris J O'Donnell; Albertine J Oldehinkel; Brenda Penninx; Alexander P Reiner; Harriëtte Riese; Arie M van Roon; John D Rioux; Jerome I Rotter; Tamar Sofer; Bruno H Stricker; Henning Tiemeier; Tanja G M Vrijkotte; Folkert W Asselbergs; Bianca J J M Brundel; Susan R Heckbert; Eric A Whitsel; Marcel den Hoed; Harold Snieder; Eco J C de Geus
Journal:  Nat Commun       Date:  2017-06-14       Impact factor: 17.694
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