Andrew Anand Brown1,2,3. 1. Department of Genetic Medicine and Development. 2. Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland. 3. Swiss Institute of Bioinformatics, Geneva, Switzerland.
Abstract
MOTIVATION: Genetic loci associated with the variance of phenotypic traits have been of recent interest as they can be signatures of genetic interactions, gene by environment interactions, parent of origin effects and canalization. We present a fast efficient tool to map loci affecting variance of gene expression and other molecular phenotypes in cis. Results: Applied to the publicly available Geuvadis gene expression dataset, we identify 816 loci associated with variance of gene expression using an additive model, and 32 showing differences in variance between homozygous and heterozygous alleles, signatures of parent of origin effects. AVAILABILITY AND IMPLEMENTATION: Documentation and links to source code and binaries for linux can be found at https://funpopgen.github.io/veqm/ . CONTACT: andrew.brown@unige.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Genetic loci associated with the variance of phenotypic traits have been of recent interest as they can be signatures of genetic interactions, gene by environment interactions, parent of origin effects and canalization. We present a fast efficient tool to map loci affecting variance of gene expression and other molecular phenotypes in cis. Results: Applied to the publicly available Geuvadis gene expression dataset, we identify 816 loci associated with variance of gene expression using an additive model, and 32 showing differences in variance between homozygous and heterozygous alleles, signatures of parent of origin effects. AVAILABILITY AND IMPLEMENTATION: Documentation and links to source code and binaries for linux can be found at https://funpopgen.github.io/veqm/ . CONTACT: andrew.brown@unige.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Authors: Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis Journal: Nature Date: 2015-10-01 Impact factor: 49.962
Authors: Tuuli Lappalainen; Michael Sammeth; Marc R Friedländer; Peter A C 't Hoen; Jean Monlong; Manuel A Rivas; Mar Gonzàlez-Porta; Natalja Kurbatova; Thasso Griebel; Pedro G Ferreira; Matthias Barann; Thomas Wieland; Liliana Greger; Maarten van Iterson; Jonas Almlöf; Paolo Ribeca; Irina Pulyakhina; Daniela Esser; Thomas Giger; Andrew Tikhonov; Marc Sultan; Gabrielle Bertier; Daniel G MacArthur; Monkol Lek; Esther Lizano; Henk P J Buermans; Ismael Padioleau; Thomas Schwarzmayr; Olof Karlberg; Halit Ongen; Helena Kilpinen; Sergi Beltran; Marta Gut; Katja Kahlem; Vyacheslav Amstislavskiy; Oliver Stegle; Matti Pirinen; Stephen B Montgomery; Peter Donnelly; Mark I McCarthy; Paul Flicek; Tim M Strom; Hans Lehrach; Stefan Schreiber; Ralf Sudbrak; Angel Carracedo; Stylianos E Antonarakis; Robert Häsler; Ann-Christine Syvänen; Gert-Jan van Ommen; Alvis Brazma; Thomas Meitinger; Philip Rosenstiel; Roderic Guigó; Ivo G Gut; Xavier Estivill; Emmanouil T Dermitzakis Journal: Nature Date: 2013-09-15 Impact factor: 49.962
Authors: Andrew Anand Brown; Alfonso Buil; Ana Viñuela; Tuuli Lappalainen; Hou-Feng Zheng; J Brent Richards; Kerrin S Small; Timothy D Spector; Emmanouil T Dermitzakis; Richard Durbin Journal: Elife Date: 2014-04-25 Impact factor: 8.140
Authors: Clive J Hoggart; Giulia Venturini; Massimo Mangino; Felicia Gomez; Giulia Ascari; Jing Hua Zhao; Alexander Teumer; Thomas W Winkler; Natalia Tšernikova; Jian'an Luan; Evelin Mihailov; Georg B Ehret; Weihua Zhang; David Lamparter; Tõnu Esko; Aurelien Macé; Sina Rüeger; Pierre-Yves Bochud; Matteo Barcella; Yves Dauvilliers; Beben Benyamin; David M Evans; Caroline Hayward; Mary F Lopez; Lude Franke; Alessia Russo; Iris M Heid; Erika Salvi; Sailaja Vendantam; Dan E Arking; Eric Boerwinkle; John C Chambers; Giovanni Fiorito; Harald Grallert; Simonetta Guarrera; Georg Homuth; Jennifer E Huffman; David Porteous; Darius Moradpour; Alex Iranzo; Johannes Hebebrand; John P Kemp; Gert J Lammers; Vincent Aubert; Markus H Heim; Nicholas G Martin; Grant W Montgomery; Rosa Peraita-Adrados; Joan Santamaria; Francesco Negro; Carsten O Schmidt; Robert A Scott; Tim D Spector; Konstantin Strauch; Henry Völzke; Nicholas J Wareham; Wei Yuan; Jordana T Bell; Aravinda Chakravarti; Jaspal S Kooner; Annette Peters; Giuseppe Matullo; Henri Wallaschofski; John B Whitfield; Fred Paccaud; Peter Vollenweider; Sven Bergmann; Jacques S Beckmann; Mehdi Tafti; Nicholas D Hastie; Daniele Cusi; Murielle Bochud; Timothy M Frayling; Andres Metspalu; Marjo-Riitta Jarvelin; André Scherag; George Davey Smith; Ingrid B Borecki; Valentin Rousson; Joel N Hirschhorn; Carlo Rivolta; Ruth J F Loos; Zoltán Kutalik Journal: PLoS Genet Date: 2014-07-31 Impact factor: 5.917