TY - JOUR T1 - Common genetic variation drives molecular heterogeneity in human IPSCs JF - bioRxiv DO - 10.1101/055160 SP - 055160 AU - Helena Kilpinen AU - Angela Goncalves AU - Andreas Leha AU - Vackar Afzal AU - Sofie Ashford AU - Sendu Bala AU - Dalila Bensaddek AU - Francesco Paolo Casale AU - Oliver Culley AU - Petr Danacek AU - Adam Faulconbridge AU - Peter Harrison AU - Davis McCarthy AU - Shane A McCarthy AU - Ruta Meleckyte AU - Yasin Memari AU - Nathalie Moens AU - Filipa Soares AU - Ian Streeter AU - Chukwuma A Agu AU - Alex Alderton AU - Rachel Nelson AU - Sarah Harper AU - Minal Patel AU - Laura Clarke AU - Reena Halai AU - Christopher M Kirton AU - Anja Kolb-Kokocinski AU - Philip Beales AU - Ewan Birney AU - Davide Danovi AU - Angus I Lamond AU - Willem H Ouwehand AU - Ludovic Vallier AU - Fiona M Watt AU - Richard Durbin AU - Oliver Stegle AU - Daniel J Gaffney Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/05/25/055160.abstract N2 - Induced pluripotent stem cell (iPSC) technology has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterisation of many existing iPSC lines limits their potential use for research and therapy. Here, we describe the systematic generation, genotyping and phenotyping of 522 open access human iPSCs derived from 189 healthy male and female individuals as part of the Human Induced Pluripotent Stem Cells Initiative (HipSci:http://www.hipsci.org). Our study provides a comprehensive picture of the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability for use in genetic studies of complex human traits and cancer. Using a combination of genomewide analyses we find that 5-25% of the variation in different iPSC phenotypes, including differentiation capacity and cellular morphology, arises from differences betweenindividuals. We also assess the phenotypic effects of rare, genomic copy number mutations that are recurrently seen following iPSC reprogramming and present an initial map of common regulatory variants affecting the transcriptome of pluripotent cells in humans. ER -