MOTIVATION: Despite recent advances of modern GWAS methods, it is still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. RESULTS: We developed an R package rqt, which offers gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone. We applied this tool to the analysis of Alzheimer's disease data from three datasets CHS, FHS and LOADFS. Test results from meta-analysis of three Alzheimer studies show its applicability for association testing. AVAILABILITY AND IMPLEMENTATION: The package rqt is freely available under the following link: https://github.com/izhbannikov/rqt. CONTACT: ilya.zhbannikov@duke.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Despite recent advances of modern GWAS methods, it is still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. RESULTS: We developed an R package rqt, which offers gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone. We applied this tool to the analysis of Alzheimer's disease data from three datasets CHS, FHS and LOADFS. Test results from meta-analysis of three Alzheimer studies show its applicability for association testing. AVAILABILITY AND IMPLEMENTATION: The package rqt is freely available under the following link: https://github.com/izhbannikov/rqt. CONTACT: ilya.zhbannikov@duke.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: E H Corder; A M Saunders; W J Strittmatter; D E Schmechel; P C Gaskell; G W Small; A D Roses; J L Haines; M A Pericak-Vance Journal: Science Date: 1993-08-13 Impact factor: 47.728
Authors: Colton Linnertz; Lauren Anderson; William Gottschalk; Donna Crenshaw; Michael W Lutz; Jawara Allen; Sunita Saith; Mirta Mihovilovic; James R Burke; Kathleen A Welsh-Bohmer; Allen D Roses; Ornit Chiba-Falek Journal: Alzheimers Dement Date: 2014-01-15 Impact factor: 21.566
Authors: Rona J Strawbridge; Josée Dupuis; Inga Prokopenko; Adam Barker; Emma Ahlqvist; Denis Rybin; John R Petrie; Mary E Travers; Nabila Bouatia-Naji; Antigone S Dimas; Alexandra Nica; Eleanor Wheeler; Han Chen; Benjamin F Voight; Jalal Taneera; Stavroula Kanoni; John F Peden; Fabiola Turrini; Stefan Gustafsson; Carina Zabena; Peter Almgren; David J P Barker; Daniel Barnes; Elaine M Dennison; Johan G Eriksson; Per Eriksson; Elodie Eury; Lasse Folkersen; Caroline S Fox; Timothy M Frayling; Anuj Goel; Harvest F Gu; Momoko Horikoshi; Bo Isomaa; Anne U Jackson; Karen A Jameson; Eero Kajantie; Julie Kerr-Conte; Teemu Kuulasmaa; Johanna Kuusisto; Ruth J F Loos; Jian'an Luan; Konstantinos Makrilakis; Alisa K Manning; María Teresa Martínez-Larrad; Narisu Narisu; Maria Nastase Mannila; John Ohrvik; Clive Osmond; Laura Pascoe; Felicity Payne; Avan A Sayer; Bengt Sennblad; Angela Silveira; Alena Stancáková; Kathy Stirrups; Amy J Swift; Ann-Christine Syvänen; Tiinamaija Tuomi; Ferdinand M van 't Hooft; Mark Walker; Michael N Weedon; Weijia Xie; Björn Zethelius; Halit Ongen; Anders Mälarstig; Jemma C Hopewell; Danish Saleheen; John Chambers; Sarah Parish; John Danesh; Jaspal Kooner; Claes-Göran Ostenson; Lars Lind; Cyrus C Cooper; Manuel Serrano-Ríos; Ele Ferrannini; Tom J Forsen; Robert Clarke; Maria Grazia Franzosi; Udo Seedorf; Hugh Watkins; Philippe Froguel; Paul Johnson; Panos Deloukas; Francis S Collins; Markku Laakso; Emmanouil T Dermitzakis; Michael Boehnke; Mark I McCarthy; Nicholas J Wareham; Leif Groop; François Pattou; Anna L Gloyn; George V Dedoussis; Valeriya Lyssenko; James B Meigs; Inês Barroso; Richard M Watanabe; Erik Ingelsson; Claudia Langenberg; Anders Hamsten; Jose C Florez Journal: Diabetes Date: 2011-08-26 Impact factor: 9.461
Authors: Sekar Kathiresan; Cristen J Willer; Gina M Peloso; Serkalem Demissie; Kiran Musunuru; Eric E Schadt; Lee Kaplan; Derrick Bennett; Yun Li; Toshiko Tanaka; Benjamin F Voight; Lori L Bonnycastle; Anne U Jackson; Gabriel Crawford; Aarti Surti; Candace Guiducci; Noel P Burtt; Sarah Parish; Robert Clarke; Diana Zelenika; Kari A Kubalanza; Mario A Morken; Laura J Scott; Heather M Stringham; Pilar Galan; Amy J Swift; Johanna Kuusisto; Richard N Bergman; Jouko Sundvall; Markku Laakso; Luigi Ferrucci; Paul Scheet; Serena Sanna; Manuela Uda; Qiong Yang; Kathryn L Lunetta; Josée Dupuis; Paul I W de Bakker; Christopher J O'Donnell; John C Chambers; Jaspal S Kooner; Serge Hercberg; Pierre Meneton; Edward G Lakatta; Angelo Scuteri; David Schlessinger; Jaakko Tuomilehto; Francis S Collins; Leif Groop; David Altshuler; Rory Collins; G Mark Lathrop; Olle Melander; Veikko Salomaa; Leena Peltonen; Marju Orho-Melander; Jose M Ordovas; Michael Boehnke; Gonçalo R Abecasis; Karen L Mohlke; L Adrienne Cupples Journal: Nat Genet Date: 2008-12-07 Impact factor: 38.330
Authors: Phoebe C R Parrish; Delong Liu; Russell H Knutsen; Charles J Billington; Robert P Mecham; Yi-Ping Fu; Beth A Kozel Journal: Hum Mol Genet Date: 2020-07-29 Impact factor: 6.150